I can't really see that being an issue unless you have a cartridge with a co-processor inside. If it doesn't have the coprocessor, the only thing it's really doing is feeding data, so loading times would be milliseconds longer. With the coprocessor in the cartridge, it *may* have issues. Maybe the system can handle timing differences, but maybe not.
Take for example Apple's idea to make a "beautiful" motherboard with straight lines only. It failed miserably, crashing consistently due to the RAM having slightly different timing, and connected peripherals getting data at different times.
So superFx games might be an issue. I'll be sure to test out starfox before I do all of the wiring and cutting. I may have to rethink my gameplan. I do have an alternate idea in mind. Maybe if things don't work as planned ill make a custom box and mount all 4 mobo's horizontal and close to the top. Then I won't even have to rewire everything, just the video and controller ports. I'm good with woodwork.