Your instincts are very likely correct. By not demonstrating eagerness to comply with any demand, regardless of reason, you are now damaged goods. However, I question your timing. My instincts honed over 25 years in the viper pit of office politics are saying you need to have an extreme sense of urgency. Don't wait to get certified, you can get certs elsewhere. It's always easier to get a new job while you still have a current job.
The cemeteries of the world are full of indispensable men.
If the company suddenly bends over backwards, gives you a signed assurances of an exemption to general policy and a raise then feel safe. Anything short of this is an invitation to Get Out Now.
I am rarely a hipster, but I was definitely on the "Musk is an asshole" bandwagon waaaaaaaaaaay back in the days of grabbing credit for PayPal and founding Tesla. He's always been an asshole, but for the longest time his very loud fan club was willing to overlook the various indicators.