Because otherwise gutting the Empire as the Ottomans would be too cheap'n'easy. The HRE contains most of the best provinces in the world (including most of the present-in-1399 manufactories IIRC), and many of them are (of themselves) quite poorly defended due to being parts of tiny minors, so there absolutely should be an exceptional cost associated with taking HRE territory by main force even if you're a Muslim.
It's easy anyway, as long as you are powerful enough a few stab hits won't stop you, or you will take "only" five HRE provinces per war and immediately take them out of the Empire by using the five available magistrates. I only screwed up because I forgot to gather enough magistrates. Not to mention that the other effects of refusing to hand over the province (+10 RR, etc) are quite punishing on their own and that creating huge empires is way too easy in general in EU III. I wouldn't mind increasing the revolt risk for all new conquered provinces and making the HRE ones even more likely to rebel than the rest of the world but the stab hit is perfectly nonsensical if you are playing a non-Christian country.
I agree Imperial provinces should be hard to take, but if you look at the text of the Formal Request and consider what's happening from a 'role-play' perspective it makes absolutely no sense. Why would refusing a Christian Emperor's demand to hand back territory you just conquered result in a loss of stability in your Muslim nation? If anything, accepting the demands would be seen as a huge embarrassment, and that would cause stability loss (and a loss of prestige) in your nation.
Exactly.