Yes, you can always just import the games again and name it a different platform or... If you just want the same games duplicated just create a playlist. Highlight all the games in Launchbox, right click and click edit/add to playlist/new playlist. If you then check "include this playlist with Platforms" on the bottom, it will essentially be treated the same as a platform.
As for part 2, since its just running Hyperspin, you can always just import the exe in the root as a windows application (without an emulator) and then just launch it directly. Like you said though, Bigbox will still be running in the background since it thinks it's a game. The only real way I can see around this would be to create a batch file or something that can kill the Launchbox process and then restart it after. That would be a big pain though and there will be quite a lag waiting for it to close and then re open again. I guess it will really depends on if your system specs can support running without bogging everything down.
What I've done before is import the full MAME set including e everything and then use Genres. Basically, use the auto create playlist's function and then go to Genres. It automatically separates games into computers, consoles, slots etc. From there you can just select all (alt a), right click and use bulk edit to change the platform for all the games under that genre. Thats how I know have an entire full MAME set but nicely separated into different platforms.
On a side note, nobody really talks about it, but MAME has a TON of goodies in it that are not arcade. Most people only care about arcade but some things in MAME are fascinating and really fun to explore and play with.
Retro_Rage's post in Noob Question- RetroBeast and KinHank was marked as the answer