I can give you a few reasons. I happen to agree with you, but Dave did note in either an interview or in the liner notes that some vocal tracks were lost (it may have just been Take No Prisoners).
The other thing I think is possible is that with the remixing remastering, there may have been settings lost in the transfer from analog to digital, or whatever they are modernizing. Some of the vocal processing that producers had up their sleeves may not have been available to Mustaine when he was reworking on these. Hell, he might not have even known about them in the first place. Also, he could have just liked his natural voice more without any reverb, echo, or any other stuff.
Anyway, thats just an idea or two