The BogoMIPS value is derived from a calibration that Linux does against the timer of choice so it could very well be a reason why.
Honestly, no idea if Krikkz's Extended SSFv2 is even implemented on MiSTer. I'd have to check but considering the rarity of it I'd be surprised if it was there.
Porting Linux to SH3 is surely easier than what it has been for SH2 (SH7604, more precisely); and considering it has 512MB of RAM you probably can just get away with a non-stripped to the bones Linux image (And initramfs, of course). It surely sounds like a good playground.