Agreed. Also, let's remember that one of the main links in Philippines were NOT fleets with mainland Spain, but with New Spain (Mexico) a.k.a "Navío de Manila", which is somewhat shorter & faster than crossing the whole Asia and circumnavigating Africa (a route that was not exactly sure)
AFAIK, there were no regular fleets between mainland Spain from the Philippines. The regular connection was always Manila-Acapulco (New Spain) ships. If a direct exception needed to be made, it was by circumnavigating South America, not Africa (not that it was any more pleasant). Spain didn't have support stations along the Atlantic-Indian Ocean route.
I should add a couple more checks I forgot.
- The Church. This was sometimes a major check. A governor, particularly those in more remote colonies, might be able to intimidate the local Audiencia into collaborating with his schemes, but the clergy were a much harder nut to crack. They were independent, very noisy and squealed back to Spain about everything and anything, through their own channels. And I'm not talking merely the usual native-lovin' hippie friars. The colonial Bishop or Archbishop was a pretty powerful figure in his own right, and had his own apparatus of commissioners of the Holy Office and courts of the inquisition. And the crown did not really try to reconcile them - squabbles between Priests and Soldiers were frequent, and the crown seemed to like it that way.
- The "
Visitador". This was irregular and unnanounced, but colonies were subject to surprise inquiries by a "Visitor", a special royal agent with license to suspend & override an Audiencia and set up his own court of inquiry (the "
Visita") and go through anything he pleased. He had the power to dismiss a governor on the spot. Theoretically a surprise, Visitadors could arrive any time. Nonetheless, they usually only came when the government back in Spain received complaints, or in the aftermath of new directives (government wanted to check if they were being implemented). So while no one expects the Spanish Visitador, they can sometimes guess.
- The "
Residencia". Another uniquely Spanish colonial institution. The "Residencia" was an end-of-term trial of the colonial governor. It didn't matter if the guy was a beloved five-star saint that blew rainbows out his ass. Colonial governors were always -
always - put through a "residencia" - an arduous trial and audit, at the end of their term, by a special judicial board, usually presided by the incoming governor. It lasted at least three months - sixty days to allow anyone in the colony to file complaints, followed by the ordeal of a thirty-day trial, going through his entire record, actions, judgments & financial accounts with a meticulous fine-tooth comb, sniffing for any irregularities, no matter how small. Given the unpleasantness of a Residencia, and its potential high-stakes consequences, I am actually surprised colonial governors who knew they might get into trouble didn't just bail the colony near the end of their term. I guess the looming "Residencia" threat counts as a kind of check - governors had better watch their step through their entire term, since any stray naughty thought can come back and bit them in the ass in the end.