I run a lot of mine in that configuration. Sitting up on thier side closer into the center of the chassis. They work fine. They seem to have a better balance left to right. Not as low of center of gravity but doesn't tilt to one side as much when jumping. If I ever get into racing and need to find that extra little that will win me a race. I might lay them down. It could just be the edge I need. LOL
Anyway one thing that helps hold my batteries a little better is I use door weatherstripping on them. When I strap them it it gives a little cushion or compression area so I can snug them down better. It really helps more on the flat chassis I have with out a tray though. Like the FLM chassis.
These are some old pics but might spark an idea how it might work for you.
Oh hey, check out my super swifter sweeper or what ever they are called. The red broom handled item to the left. I took it put some little wheels on it and attached the magnet from a 75 watt pioneer speaker to the bottom. Drop a 3mm screw on that tile patter and it's gone if you take your eye off it. I use to waste too much time looking for them. Now I just get a different screw from the bench and later on. Take the swifter and run it around a few time and get back a bunch of my screws, bearings, body clips, all kinds of metal things. Treasure hunt.