Fester...
Why not just put the entire country under one zone? That effectively does what you're looking for.
Also, I do believe strat still affects resupply like it use to but on many maps the only reason strat/HQs come up so fast is because there are GVs resupplying it. Hence, nullifying the bomb run. Don't put GV spawns to resupply strat and it's back to waiting for automatic supply or C47 supply.
Edit:
I just re-read your post.
I believe the reasoning for captured bases taking longer to re-supply is that it would take longer for the capturing country to get supplies to a distant base. The solution is to run supplies by M3 or C47. I've seen this done many times and the base is up within 15 minutes or less.
With mulitple zones, capture the zone base and your resupply time is down to the normal 30 minutes.