It can be used to charge batteries or run equipment that that powered that way.

Probably, for regulation purposes, you want to have a 12V (nominal) battery attached to run equipment for a bunch of reasons. It appears to taper the charge at the end when you reach a "finishing" level.

It really is "okay" to keep the system. You'll just have to replace your gel cell batteries more often and you'll not be re-charging them that quickly, and they'll have a lower amount of effective amp hours than you should. BUT, that may be okay with you.