The real secret weapon of MiSTer is having the analog video timings recreated for dozens of hardware platforms without needing dozens of pieces of hardware. It's pretty difficult to convince yourself that an SNES is being displayed as-intended with emulation.
If you're considering a MiSTer then you likely have enough disposable income to find and home a CRT, which is where I think draws the majority of the value of the MiSTer out.
Granted the last time I looked at retroarch there were options to handle this and the CRT simulation shaders are in a great state.
At the end of the day the pixel aspect ratio will not affect the gameplay. Hell, there are counter strike players today that still play with incorrect aspect ratio pixels (4:3 render resolution stretched onto a 16:9 display) for no reason other than "some players did it at tournaments ten years ago".