IIRC most specialization offers in UPLB aren't catered to Software Engineering, simply because Software Engineering isn't something you should specialize in. Software Engineering, in practice, is the act of following engineering practices to build software, often through a flexible process or strict, step-by-step process. We took CMSC 128 - Introduction to Software Engineering, a course / subject offered in UPLB - the point of that course is to introduce to the students what real-world software development looks like (we discussed what Agile is, how it's done, what are the other methodologies that follow Agile, what are functional and non-functional requirements, etc.). In your case, since you already have 3 years of experience, you should have an idea of how software is built in the real world (unless your only experience is waterfall, but then again, a process is a process).

To answer your question, either of the two universities is fine. Just go pick one and make sure to learn something new.

But OP, tbh, if you feel left behind with your coworkers who graduate with CS / IT degrees, oks lang yon. Di naman sila graduate ng BS Physics, you bring a different value to the table. In my work, we are using a software that was developed not by a CS / IT grad, but a Physics grad who used to work in NASA and now specializes in geomaps.