Nothing, it doesn't interact with personal equipment because there's no way to make it work. You can get a fleet of merchant ships, but you can't convert that into a level 20 (or 10) weapon.
If you want it to interact... so the rules prevent you from upgrading your ship to the next higher tier than your level, but if you wanted to allow the 'worlds' to spill over. You could rule that if they get enough BP to where they would have enough to upgrade up to a higher tier (when they get high enough level), you could soften the normal level restriction on goods and start allowing them access to higher level gear by a level on the personal market, than they had before.
You could charge them a BP for the privileges, or simply have it be a general goal, and maintaining that extra capital keeps that higher equipment available. (that way, when they do level up, they are already ready to be able to upgrade their ship to their level in tier)
That is, to be fair, the intention.
I understand what you are saying, but the issue I see is that my party will not have the credits to purchase the higher level equipment because they aren't earning creds for hauling cargo. So really, cargo running is not a viable source of income for my party. More of just a means to upgrade their ship when needed.
That is, to be fair, the intention.
However, there is nothing preventing the GM from providing credits (or "free" items) and experience rewards in addition to the BP earned with the cargo subsystem. Making the checks and/or dealing with the difficulties could be used along with the side jobs to present a more "organic"/"sandbox style" campaign than the standard "adventurer" paradigm.
There’s never anything preventing a GM from doing that for any or no reason.
True. However, the cargo subsystem is not, in and of itself, a replacement for the "normal" credit and experience rewards.
What I was outlining is that the GM can use the cargo subsystem as the basis (with additional effort) for a "Drift trader" style campaign instead of the usual adventure path. Which seems to be what the OP is looking for.
My take is pretty similar to Dragonchess Player's: You can't give player characters weapons and equipment with BP directly, as there is no credit-to-BP ratio for a good reason, mainly to stop players from pawning their starting ship for a pile of credits. That being said, there's no reason the players can't make credits in addition to BP with their cargo trading and side jobs, either as bonuses when selling cargo or as extra stuff found among their cargo purchases.