Wood – Will the raised flower bed design be sturdy enough

Pocket screws are NEVER adequate for structural support. Something like this bed should be assembled with lags and carriage bolts, or better yet, Simpson brackets. Having said that, the most important joint in this piece is the connection between the bed rails and the posts so you could just use a combination of ship laps and bed bolts at those intersections. Glue and screw the ship lap together but don't glue the long rails. This will be strong but allow you to disassemble the frame into manageable pieces. I also think you should consider adding cleats to your ladder rungs to keep them sturdy. Cheers!

The Easy Way

Fortunately, you're holding up a model train, not an actual train, so you can take some liberties.

The hard part is following the rounded, off-square corners; the easy way to work around that is to literally cut corners. Rather than attempt to follow the rounded corners, just install four shelves as long as the straight parts of each wall, then measure and cut four trapezoid shaped connectors for the corners. Just about any method would work to join the trapezoids to the main shelves since there's not much weight to support. You might use pocket screws, maybe half lap joints if you have the router etc. available.

The Hard Way

You could do some geometry, measure diagonals, get out a protractor, etc. etc., and find the angles. You may even be able to use an app that works with your phone to determine the layout. But in my experience these things don't end well :)

Here's how I picture doing it ... be warned, these things don't always work the way I pictured it.

Install your shelf brackets first

You'll want to rest the shelves on the brackets as you figure things out. I'd place them all on the straight (not rounded) part of the wall, but try to get one as close as possible to the point where the wall starts to round.

Make each shelf as if it was going to be the only shelf

This will be the most time consuming step.

Use a contour gauge, make a pattern out of cardboard, and cut each shelf to hug the rounded part with a jigsaw or coping saw. A rasp may be handy for fine adjustments. Be prepared to spend some time and possibly waste some material.

Err towards removing less material and you'll be less likely to have to scrap it and start over. Remember that a 5-6mm gap will be fine, you're not machining an engine block, you don't need thousandths of an inch precision.

Look forward to the steps where these shelves are cut to fit - don't waste time fussing with a good fit in the portion that's going to wind up cut off.

Lay the shelves in place and mark intersection points

This step is easy but it's the key to the layout. Lay the North and South shelves in place on the brackets, then lay the East and West shelves on top of them. Mark the inside intersection points in each corner, on both shelves.

Cut the East and West shelves

The exact angle isn't important, you don't have to bisect the angle perfectly as long as you start the cut from the intersection point. That will be the key to making these fit nicely.

Mark and cut the North and South Shelves

Now you're coasting... put the East and West shelves back on top of the North and South shelves and mark the cut lines.

Check the fit, and fasten the shelves to the brackets, and you're ready to put tracks on it.