I think the advice you received there is correct -- you most likely didn't harm the plants by taking off the bottom leaves, but you have put several large plants in a very small space. You'll need to do a lot of pruning to keep up with them. (To that end, why not just keep the middle square's Big Boy and not prune it so heavily? You could end up with the same yield with a lot less work.)

How tall is your trellis? Big Boy plants can get huge, so hopefully you planted them very deeply to establish enough of a root ball to support the top. If it's a short trellis, you may find you have a lot more plant than you have support for.

The plants will dig their roots into the native soil underneath the bed, so that part shouldn't be a problem, but angling the plants will have no bearing on what direction the roots will grow. They will spread out everywhere.

Whatever you decide to do, take good notes for yourself and make adjustments next year, as needed. That's half the fun of gardening to me, trying new things and figuring out what works for you.