So I use a retropi emulator and select is my hotkey so if i push that and start i reboot or select and b i reset etc. Has anyone else been able to find a way to get the good house seed with this issue? or is there no other way?

The house manip works differently depending on what you're running it on. I know for my NES, I only have to hold start. Other consoles/emulators need different button holds. I don't think anyone has tested retropi, so just test different button combos.

I cannot get the manip on anything but a Front Loader NES. My top loaders i cannot do. It works power on. Retro Pi's were not really a thing when we found this.

Which emulator is loaded onto the pi? That could be a place to start, though I can't remember if emulators were tested or not for RNG manip.

When i first started doing it I was running it on emulator. So it definitely works on emulators.