Some hotels are known to not upgrade Bonvoy elites using an Explore rate (i.e. in violation of program terms, since Marriott has decided that this is an “eligible” rate for Bonvoy purposes). Even at a hotel with such a reputation, other Bonvoy status-linked entitlements, such as breakfast, will be forthcoming.

That aside, basically no downsides - most hotels will treat you in line with their usual practices (good or bad) and you can sometimes end up saving quite a bit.