For instance can I put my run of 16 star with no LBLJ into the extension category for that specifically and also the general base game 16 star category?

there shouldn't be a rule against it, but that's up to the mods. i would just submit it in both and see what happens.

In this particular instance, I know the mods are ok with it. Even though the No LBLJ CE boards are meant for people with a 16 star LBLJ run as their main PB, the mods don't question submissions to both if you used the No LBLJ route. Other games you'd definitely be better off asking in the game's forums or their discord because some boards may not allow multiple submissions like that.