Since you're living on our own bus you can simply emulate autoconfig for your onboard devices and start to pass it to the mainboard once you're done (think we had that before) - no need for hacks.

That CDTV hack you mention seems to be faking autoconfig where it isn't possible for real (pretty dumb to miss that since autoconfig just takes a single gate per slot). There must be a little more to it than that - you'll need to do the fake after the last (real) board is configured (otherwise they'd be trying to configure simultaneously) - I guess it isn't too easy to detect the last board but there probably is a pattern to react to.
_CFGIN doesn't time out, it's more beautiful than that. _CFGIN is driven by the previous _CFGOUT ORed with the previous(!) _CFGIN. _CFGOUT is pulled low by the mainboard but driven high by an unconfigured board - that way delaying the _CFGIN for the next board if present.