So why nothing totally inside the trunk? He cleaned too good?
We don't know the complete list of evidence LE already had prior to obtaining the warrant to search the house and grounds where EA lived. LE only has to explain or offer enough reason for probable cause that there was a crime committed by the subject (EA in this case).
LE is BUILDING a case and believes more evidence will, or is likely to, be found by searching where the warrant specifies.
Clues within the affidavit are - LE is looking for the clothing EA wore when seen with Christina in the garage (explained is, even if clothing was washed, it is still likely to retain DNA evidence).
Also explained, since EA's phone was wiped clean prior to its return to Sprint, LE wants to look for evidence of the phone's content on the home computer (spelled out is, uploading a phone's content to a computer hard drive results in a phone being wiped clean).
LE isn't sure if they'll find all the evidence they are hoping to find at this juncture.
LE is requesting legal permission to move forward with the investigation due to the likelihood they will collect additional evidence to support their theory that EA is the perpetrator and is responsible for this crime.
The evidence the car turned up, along with the garbage pulls, led LE to seek additional evidence by searching EA's house and grounds, the results of which we do not know yet.
The search may result in the evidence LE is hoping for or it may not provide any additional solid evidence at all.
We have to wait and see.