Is masonite harder than MDF? 
Good question, I'm not really sure?
I think masonite is denser, at least in thin pieces it is quite stiff compared to MDF. Almost like layered mica with long fibers whereas MDF is sawdust. The glue used is probably less (or at least different) and makes for a decent edge IMO.

I like your method of stacking with the dowels, but if I can make use of parts that can be completely routed out (no pesky sharp inside corners), I'll do that. I've laser cut box inserts (curved finger cutouts) directly in 3/16" (4.7625 mm) maple, but hated dealing with the cooked edges. Much faster and cleaner with the template and router table pattern bit. Also same effort if I went thicker.

I'd love a good 50+ Watt CO2 with a long focal length lens for cutting thick stuff (especially plastic) as that would be useful for so much stuff, but then there are the fiber lasers which can do metal, etc.