If all the remaining south of Tay juniors move over, there will be 59 clubs. That can then be split into a 16 team Premier, 16 team First Division and 2 regionalised Second Divisions, meaning there are 5 spots left for amateurs to make it to a 64 team structure. Once that's been achieved, I think it does make sense to link up with the amateur leagues, possibly in the same way as promotion/relegation is done between tiers 10 and 11 in England (tier 11 is effectively a collection of amateur leagues that have at some point been put at tier 11 in the pyramid). Down there, tier 11 clubs have to indicate by a certain date whether or not they want to make the step up to tier 10. The teams that want to get promoted will (providing they match the requirements) fill the promotion spots in the order of how high they finished. If there are fewer eligible teams wanting to get promoted than relegated teams from tier 10, one or more relegated teams will get reprieved.
There is no reason why something like that can't work in the East of Scotland.