Since everything is controlled digitally now, it's possible there's more information taken into account in determining which rides are eligible for multi-experience passes. For example, maybe if you have a FP for Indy and it breaks down, but the standby wait for Space is relatively good, the system will let you use your new pass for Space. But if the wait time for Space is already out of control when Indy breaks down, the system won't include Space as an option so as to avoid swelling the FP line and slowing down standby even more. Or maybe if Space already broke down earlier in the day, meaning there are already tons of anytime passes eligible for Space floating around, the system won't give out any more that day. Just a thought. We seem to be getting inconsistent reports on which rides are eligible so I would guess that either they're still playing with the system and testing scenarios, or there's another factor being taken into account that we don't see.
As for whether the passes obtained when a ride breaks down during your window (as opposed to breaking down while you are on the ride) can be used for non-FP rides, that seems like a CM discretion and/or training issue to me. If the passes don't list those rides I doubt it's technically permitted, but it might be one of those unofficial loopholes, like how they didn't used to enforce the 1-hour FP window. Or training might be inconsistent since the system is so new.
I'm just speculating here. I haven't even used MP yet so I have no genuine experience to go off of.