Nate - that all looks nice in theory, and honestly some of it goes over my head a little bit, but (1) I think you're overthinking it and (2) that seems to me to be based about 80% on theory and 20% on sim observation. I think you're making a lot of inferential leaps about how the SIM works. But I'll make two relatively simple points that hold true in my experience. First, PF/FTA are sometimes more effect than cause - for example, good teams will shoot more FT/foul less as a result of being ahead at the end of games more often, not necessarily because the team makeup causes those things. Second, I really don't think it's possible to push your number of FTA significantly higher by drafting lots of FTA. The main influence you have on PF/FTA is drafting as few fouls as possible for your own team, in my experience. In that sense I understand winning the "PF battle," but I don't think FTA impacts that much.
How about this: I'm pretty sure that teams' FTA:FGA rates don't vary a whole lot in the SIM - even if you draft lots of high FTA/low FGA players, you'll still end up pretty close to the average (and as a result your players will shoot significantly more FG and significantly fewer FT than in real life). I'll bet if you look at a recently completed league you will see teams clustered pretty close together in that measure, and you won't see a huge effect for teams that drafted a lot more FTA than others.
Just remember this: the numbers of free throws a player attempts is highly influenced by his usage. This is why low-usage guys with high FTA usually will fall far short of their RL totals (take Cedric Maxwell, for example, who I almost picked last round - he'll be lucky to shoot half of his real-life FTA in most seasons, but will usually far exceed his RL FGA). Conversely, guys who have usage that's a little higher with low FTA will usually have a very good chance of meeting/exceeding their FTA totals. So it's not just that everyone shoots less FT at a similar ratio to their RL totals - low-usage guys will usually see a bigger hit than high-usage guys, and the high-usage, low-fta guys will sometimes even exceed RL totals.
Here's three players from my current ODL team, to provide a case study:
Artis Gilmore: 19.6% usg, 559 RL FTA, on pace for 365 FTA (65% of RL total)
Tracy McGrady: 35.1% usg, 726 RL FTA, on pace for 656 FTA (90% of RL total)
Al Horford: 21.9% usg, 208 RL FTA, on pace for 225 FTA (108% of RL total)
So: Gilmore, who has pretty high FTA for his level of usage, will not get anywhere near RL FTA. McGrady, who has huge usage but also pretty big FTA, will get decently close to his RL total. And Horford, who has very low FTA for his usage, has a good shot of actually exceeding his RL total.
Remember, this will also be influenced by your total number of FTA, thanks to diminishing returns on FTA in the SIM (i.e., if you draft 5000 of them, you're not going to shoot anywhere near double everyone else in the league). So if you draft several high FTA guys, they'll probably all have trouble getting anywhere near RL. If you draft a team with really low total FTA, they might all significantly exceed RL. But I think trying to draft a bunch of FTA to significantly improve your own FTA rate, if that's what you intend to do, is not likely to pay off.