Hey there STAT, congrats on your CERT acceptance! Here's my personal take on your questions:
If you absolutely cannot take the MCAT prior to CERT starting, then that's fine. A bunch of us are taking the MCAT this summer (after CERT ended) and are still applying this cycle. Your MCAT, in my opinion, has nothing to do with if you want to pursue a master's. I'm assuming you're not going to do CERT and apply to med schools concurrently. When would you plan on applying? right after CERT ends? In which case, you will have a gap year. It's up to you with how you want to use that gap. Ideal situation for you is that you kill it in CERT all year. Start MCAT prep spring semester. Go even harder on MCAT prep once CERT is done, and then take your MCAT in May/June. And hopefully your med school apps will be sent by then.
People who do the master's are typically those who genuinely want a master's degree, and have found a research lab that they're really interested in working. There may be some students here and there who may not have done as great as they wanted during the CERT year, so continuing with the master's could possibly aide in getting a GPA boost (assuming they do well in the classes they sign up for).
For my class year, balancing spring academic matters and MCAT prep was doable. But that all depends on how you did fall semester. If you kill it in fall, spring semester won't be as bad in terms of class load. However, if you didn't get the GPA you wanted in fall, then you'll have to take on some extra classes to help get that boost during spring. Does that make sense? However, I'd recommend calling the CERT administrators and ask if there will be major curriculum changes for your class year. All my experience I just listed had to do with how our curriculum was structured.