Here's my take on why one is acceptable and the other not. Should the sim place emphasis (or more emphasis) on additional factors (# of steals, speed)? Certainly. But after taking second or third, the 1/1 60 speed runner is no more likely to score on a single or fly out than a 0/20 60 speed runner. There's an advantage gained, but it's marginal and can be a detriment compared to drafting a same-price 2/8 80 player. The programming could be better, but is not ludicrous.
The first-and-third bunt was clearly programmed wrong. There is no allowance for the runner at third to hold; that should not only be possible, but should be the default result. Most first-and-third bunts with no H&R on should result in runners at second and third and an out. Without doing the research on RL, I'd guess that a result of bases loaded with no out on the play would be more likely than the runner at third scoring. For first-and-third with H&R on, there should be a mix of runs scoring, runners out at the plate on a missed bunt, and the occasional pickoff (with the runner at first moving to second). Has anyone seen a caught-stealing-home on a bunt attempt? I've played 40,000 Live games and don't recall one, and think I've seen 3-4 pickoffs at third. For some programming reason, IF in doesn't do a damned thing for the first-and-third bunt, though about 18 months ago they did fix a glitch that had ignored IF in for other squeeze bunts after I sent them examples of dreadfully slow runners scoring all the time on bunts when they were the only runner. They told me at the time they could only make simple fixes (which that happened to be), but that most of the code was too interwoven to mess around with.
The 1/1 SB draftee is taking advantage of a pricing anomaly, similar to grabbing players who normalize up for power and watching them hit 24 homers instead of the 12 they hit in RL, drafting catchers wih D- Field ratings because the sim takes that useless rating into account, or avoiding some players because their secondary-position D/D rating inexplicably boosts their cost.
If the 1/1 runners bother you, there is a way to defend against it — draft Yadier Molina. If the squeeze bunt bothers you, the only defense is to let those games sim.