This was, in effect, the exact situation I was worried about.

I'd say first that likelihood of them saying anything will depend a lot of if the passport is valid for visa-free travel to the EU. Like I would say they're not going to be looking through stamps on a US/Can/UK/Aus/Japan/etc... passport. Maybe a second tier of allowed countries that might get a closer look, thinking in particular of Brazil and Venezuela in this case.

The rules are the same for all non-EU/EEA/CH passports past 90 days but there is a certain reality at border crossings of who actually gets more scrutiny.

Now in our case, considering it was a Cuban passport, I'd be pretty sure they'd take a closer look no matter what.

To get to the actual answer of your question. I'd have no idea and I suspect legally it gets down the idea of administrative silence in Spanish immigration law. In certain circumstances no response is a positive and other it's a negative. Regardless, it all seems rather complex and not something I'd be particularly interested in arguing with my limited French language skills, particularly in terms of the law (I'd basically just be clumsily directly translating everything from Spanish).

All of that said, if you really wanted to go, I'd recommend just driving. I'd say the chances of a road border control are much, much lower and if you see there is one you can even see if you can just turn around and not go.