A table entry is usually created after a model is done, or at least after it has been well defined. The table only refers to names in the POF typically, placements of those things are controlled in the model, and statistics for those things are in the table. So a turret's location and movement is defined in the model, the weapons loaded into the turret are defined in the table. A subsystem's name, location and size are all in the POF, the hitpoints and other flags are in the table. It depends on how you want to modify an existing model. A lot of modifications can already be done in PCS2. Complete geometry makeovers can be done without editing a table file though, as long as subsystem names are maintained. You may wish to add features to a model that require adding entries to the table though. But the original retail table info will usually suffice for most edits I think. Also, you won't need to recreate a VP file to replace a retail model. Just create a mod folder, put a data folder in it, and a models folder in that, and drop the model there. If it has the same name it will take precedence over the VP model.
BSP caching is something that PCS2 does already as well, but unless you maintain the same versioning, going between the two apps will still entail a regeneration of the data every save in PCS2 at least. Also, allowing people to simply keep the cache means that it could easily become unreliable, when people cache the BSP even when your bspgen has been upgraded. Using the same code to decide if it should be updated automatically would be best.
BSP generation is entirely dependent on the complexity of the model, and as that increases, it only takes longer. It could take 10-30 seconds for a sufficiently complex model, maybe worse for works of art like Omni's Battlestar or Brand's ISD, and that's on a fairly modern computer.