in fact, robiza has done all the video work on c64. I mainly cared about carts and tapes and memory banks (and to some extent floppies, until Curt came and made it better and faster)
and I know that flags can have problem with video updates, but I'm not so sure I can handle a complete rewrite by using timers at the moment, while I was more than capable to improve the original code until reaching the current level of accuracy (which is not bad, all considered)
now that the problem has surfaced, I added to my todo list the investigation of a timer-based rendering rewrite, but it won't happen anytime soon (especially because the current code is good as long as you don't frameskip, and it works pretty well even when you skip frames if the game is not too strict)
snes is definitely more in need of CPU timing fixes than this RTO flags problem...