Given PA/IP positively affect player development, does it make sense to have autorest thresholds lower for your top prospects on the offensive side, and maybe up the pitch count for pitching prospects? At what point does the increased injury risk factor in?

Injury will set them back far more than the missed playing time by resting them 3 or 4 games every couple weeks.  I try to give them occasional rest to keep them as close to 100% as possible.  I wouldn't play a top prospect if they got below 95 or so.  Others will probably go lower.

I might be heading a bit offtopic here, but has anyone really notcied dimished abilities bypositions players or greatly increased injuries when playing them below 100% (say 90 or 85). I had a player this season in FYC who, due to a pennantrace that wasnt over until the final game and him being my best hitter, I played all the way down to 89%. I made the playoffs, and even below 90% he hit three home runs in the first two playoff games. I am starting to believe that the idea of keeping everyone as close to 100% as possible is a bit silly, and maybe you should just try to keep guys in the "green" (above 90).

Green means go.

On the same team, I started my best SP at 100% in Game 2 of the playoffs and he threw 8 shutout inings. He was at 97% for Game 5 so I went with him and he got rocked.

I used to run my minors like I do my majors, trying to keep prospects above 95 (I try to keep my majors above 98 except down the stretch in pennant races, like Mike).  Lately I've been letting my prospects get down to 90, especially at the end of the season, to maximize playing time, and I haven't had any injuries.

I've let fringe prospects go as low as the 60's, and top prospects go into the 80's. It really depends on the player. If a guy has a health rating in the high 90's, you can be a lot more cavalier about his playing time than you can with a guy who has a 40 health rating.

 It seems like most players get to where they're going with normal playing time. This is just a guess, but I would think the extra playing time would get them there faster, but no further. Not worth the injury risk IMO.
It may be worht trying with some of those DITRs orplayers who were hurt early in their development and appear to have no chance at meeting their projections.

Carrying an extra middle fielder, corner fielder, a 3rd catcher, and two or three extra pitchers on the inactive list will give you the depth to keep everyone 100%.

This is a battle I've never quite totally figured out since I started playing this game.  Should you play your best prospects below 85%?  91%?  97%?

What I've been doing is evaluating each prospect on a case by case basis.  A fringe prospect (a guy who would barely make my ML squad or figures to be one of those guys who gets called up at roster expansion and sent back down at the end of every season) I'll play him until he drops dead because if he gets hurt, oh well, he wasn't going to figure much into my future anyway.  A "B" prospect , like a guy who would be a platoon player, defensive specialist, super utility player (can play multiple positions and maybe has good speed and/or eye), I'll play until he's about 93 or 94% then rest him until he's 100%.  For my best prospects, I keep a very close eye on them.  If they have good health and makeup I'll let them get into the 93-94 range before resting them back to at least 98 but preferably 100%.  If their health or makeup is questionable, then I'll try to rest him once he gets to 95 or 96. 

Once the MiLB playoffs start, I'll let them play every day no matter what their energy level is, just like in ML playoffs.  I'll roll the dice to get them as much PT as possible. 

Strategies to rest guys better?
1) platoon the prospect.  Only start him vs righties and put him on the bench vs lefties, then, late in the season, start him every day.
2) make sure he's last on the player rest chart and possibly defensive replacement chart.  Take him out in the 8th inning.
3) If you micromanage your minors, inactivate him during the stretch of the schedule where you are playing very weak teams.  Lots of guys don't manage their miors very well or at all, so if you've got a 3 game series against a team with a bunch of 0(0) pitchers, inactivate your best prospects for that series then reactivate him when it's over.  If you're facing 3 straight 0(0) pitchers, in those 3 games your prospect might get 24 ABs.  Good time for a rest.
4) Bat him lower in the batting order even if he's a really good hitter. I guy you might normally bat 2nd or 3rd, bat him 6th.  He'll get approximately 60-70 fewer ABs over the season, so he rests a little bit more.