Your points are valid. It seems odd to me because Werter's credentials sound pretty decent. I expected more. His relationship with Steven Brown, who worked for Crystal Sheffield seems pretty strange to me. I also wonder about his meetings with Misty Croslin's lawyer.
I've listened to almost all of the audios of Tommy's phone calls and a fairly consistent picture emerges of Tommy. A recurring theme is his longing for his wife (now ex) and children. Another repeated element is his statement that he had no involvement in the disappearance of Haleigh. He fully admits that he was terribly wrong in getting hooked on drugs and that, when he gets out, he will never, ever do drugs again and will get an education and get a job. (Same things Misty is saying :waitasec
Tommy keeps saying he can't talk about the case, but he occasionally does. He is inconsistent in who he blames for taking/hurting Haleigh.
At one point, he insists it's Ron and that he (Tommy) saw Ron do something but Ron didn't know this. Then later, several times, he puts the blame on Joe. He says that Nanny's a liar and that he didn't tell her any of the things she says he did. Yet, he did admit that he took LE to the dock. There may be some validity that he doesn't remember or is mistaken about some things because of his drug use at the time.
I get a very different vibe from Tommy's lies than from Misty's lies. Misty's lies seem more planned and conniving, whereas Tommy's are more defensive. He doesn't come across as the brightest tool in the shed, but neither does he come across as mean or vindictive. He is most certainly depressed in a lot of his calls (as is his father).