Personally, I would have a "window" in your dome, perhaps an appropriately sized hole that you could pop a rubber, plastic or stainless cap/plug into it, that will allow you to push that top shock bolt through in the event you get a failed shock/spring.

Likewise for the battery, you should give serious consideration to mounting it so you can access it through the trunk rather than from underneath. Perhaps build a box with a flange as discussed earlier that will drop through the floor in the same location you're already thinking of (especially easy if you use the smaller sized driy cell battery). Put a nice lid on it, and cover it with carpet. If you use the car like many of us, you'll be putting a charger on it at least a couple times a year, likely more. Or when doing some maintenance or "improvements" you'll need to disconnect power occasionally. Find your opportunity for exercise elsewhere.