I have a hard time believing that Jodi left the house during this time because it would have taken out of her control any ability to orchestrate events or steer Travis' activities. If she left the house, Travis could have left to run an errand, or invited a guest over or talked on the phone about her being there. I do not believe Jodi would have taken this chance.
However, I do believe that Jodi was not directly in Travis' presence for some portions of the afternoon -- during those times, I believe that she was making her murder preparations
Here's what we know happened between 2:00 and 5:00 that afternoon:
We know Jodi changed into her murder clothes.
We can infer that Travis got dressed in his garments, long gym shorts and a T-shirt because those were the clothes that were put in the wash and presumably the clothes he took off to take a shower at 5:20.
We know Travis was on his computer at 4:00 sending an email. The last computer activity is from Travis' email at around 4:00, and his cell phone was down in the office, so I do believe Travis was on his computer that afternoon right before the shower pics.
We know that Travis shaved at some point before he took a shower - he looked to be very recently shaved in the shower pics, so it's likely he shaved after he was on the computer at 4:00.
We know that the bed linens were stripped and washed.
Here's what Jodi has said happened after 2:00, and some of these descriptions indicate that Jodi was not directly observing what Travis was doing at these times
Jodi said she showered and that Travis was out of the room. I think it's likely this happened because it's a good way for her to remain in his house for a legitimate reason -- thus stalling until the murder. We don't know what Travis was doing during this time or at what time she took a shower.
Jodi said that she took her suitcase, camera, backpack, and laptop to the car after 2:00. In her ninja story, she mentioned grabbing her backpack and purse on her way out - I believe this is what happened, and I believe that she needed her backpack in the house because she had her murder paraphernalia and post-murder clothes in there. Also, she was very evasive about this in her x-exam and could not describe any details or what Travis was doing at the time. On the other hand, it makes some sense that she would want her belongings to be out of the house so they would not get murder residue on them.
Jodi said she and Travis were in his office on the computer looking at photos and having sex - I believe this was said to have happened after their bedroom escapades. This may or may not have happened, but I believe there was at least some time that Travis was in his office, on his computer, at some time without Jodi being immediately present. I believe this because in her interview with Flores she does not know what Travis was doing while he was on his computer.
Jodi said Travis was cleaning his house, but she could not even describe where she was sitting at the time. He may have been cleaning his house, but she was doing something else - some kind of murder prep or possibly showering or placing the gun and knife in the cabinet under the sink. She may have pretended to be napping.
At some point that afternoon Travis shaved, but Jodi said she did not think Travis shaved that day - but I think she was lying about this. I believe this happened right before he took a shower because he looks freshly shaven in the shower pics and I think most guys would combine shaving and showering in one bathroom visit, rather than doing these things separately. Remember that Travis' roommate was home between approximately 3:00 and 4:00 that afternoon, and certainly Jodi would have been acutely aware of when the roommate came and left. When the roommate left at around 4:00, same time as the last activity on Travis' computer, I believe Jodi then convinced Travis to go upstairs to take pictures of him shaving -- this took quite a bit of coaxing, according to her. I believe Jodi took pictures of Travis shaving with her own camera, and this is why there are no pictures found on Travis' camera. Not sure about this one, but Juan's questions lead me to believe that they may have some evidence on Jodi's camera.
Jodi said they gave Napoleon a bath after 2:00 that afternoon - but I honestly think she cleaned Napoleon off after she murdered Travis, maybe because he had blood on him. I believe this because she mentioned giving Napoleon a bath to Flores as a reason her blood and hair would be at the scene (?), and the roommates said the doggie gate was across the stairs, and that was unusual - presumably to keep Napoleon away from Travis' room -- this would have been done by Jodi without Travis' knowledge, so I believe she did this after she murdered Travis.
Jodi said she ate a banana. There is some indication that they were in the kitchen at some point because Travis took off his CTR ring and left it on the kitchen counter.
What does this mean?
IMO all of this means that Jodi did not leave the house because she would not give up that kind of control of Travis' environment right before she planned to kill him.
It also means that there were times that Travis and Jodi were not directly in each other's company for part of the afternoon. At those times, I believe Jodi was setting up for the murder -- I believe that she put the gun and knife in the cabinet under the sink, and that she was crouching there taking pictures immediately before the first "inadvertent" pictures were taken.
I believe that all of the activities that afternoon were steered and directed by Jodi - I think she suggested that they go down to the office to get on the computer and look at pictures so she could hear the roommate's car when he left. The office was right next to the garage and within earshot of the driveway. I think she suggested that they wash the linens, or maybe took that upon herself while Travis was doing something else in the house, because she intended to remove her DNA from his linens.
I think she coaxed him into taking pictures of him shaving right after she was sure that the roommate was gone, and she did this because she had previously taken pictures of him shaving and knew he would be agreeable because he had like the previous pictures she had taken of him shaving (he had used one of those pics for his MySpace profile).
I think Travis may have wanted to take a shower earlier in the day, but Jodi precluded this by saying SHE needed to take a shower. Travis, being a considerate guy, allowed her to take a shower first.