I didn't really follow this. My suggestion is:OK, so you are saying big rocks and/or rock & mortar is the way to go??? I gotta tell you, it was heart breaking to see all my 12" wide rocks floating right along side my rubber and fishes! That is why I just stayed with a felt bottom after removing the rubber... nothing was floating! Maybe a combination of hoses, non'flat bottom, strategically placed boulders....??
1. Cone shaped bottom. Not ice cream cone, just a nice slope, maybe 1" per 1'.
2. Drain pipe as vents. Covered in sand on the bottom.
3. Mortared rock covering the entire bottom and up the sides a bit. Stay 1' below the water surface with the mortared rock. All the way to the surface can be a problem in your climate. Keep the rock below the normal freeze line.
Strategically placed boulders is definitely NOT the way to go. These would dimple the bottom leaving bulges of liner between the boulder which is a perfect for collecting gases. Unless maybe you're talking about a 1/2 ton boulder in the center at the lowest point.
I'm not saying this is a guaranty fix. Saying it reduces the risk.