He's guilty, and he pleaded guilty. My guess is that he will get some prison time.
DOJ prosecutes tax crimes usually, not the IRS. Special counsels are so rare, it's not fair to say what they "usually" prosecute.
Again, take the politics out of it: Manafort is a tax cheat, and he got caught, and he got prosecuted. We don't know what kind of deals were offered. I read somewhere that people describe him as an adrenaline junkie -- he may just have refused all deals for the rush. Some clients are like that. But I don't think you can attribute sinister motives to thee government -- they had a case, they had witnesses, they had documentary evidence. Manafort's defense team did what it could with what it had, but in the end I don't think it's going to be enough.
There will be another Manafort trial soon. Let's see if deals are cut for that one.