Well, it would be convenient to have a prison with larger capacity which still fits in one base tile. Your argument of "by the time you'll have it, prisons cost pocket money" is flawed because it forces the player to waste a much more scarce resource than money: base tiles. "Just build more prisons" doesn't really work when we need more of everything with the kind of facility sizes and variety we have in Piratez (more living quarters, more voodoo schools, more gyms, more study rooms, more storage rooms, more different research/defense facilities because research/manufacturing projects require XYZ on site and sick bays too). Of course, one doesn't need all of that, but the more facilities there are, the more valuable base tiles are and the more wasteful it becomes to have duplicates which are usually not serving a purpose (ie prisons which are most often empty because everyone is enslaved, but present because once in a while you get too many prisoners).
Because of this value of base tiles, I generally try to make do with 1 in every base that has an active raiding team, plus 1 in my storage base for the VIPs I am keeping for later. More tiles dedicated to holding prisoners doesn't make sense and I'd happily throw money at the problem if it were possible to solve it this way (ie build an expensive cryo-prison which also requires expensive electricity to power it). Especially since by the time you would get a high-tech prison, you can tank most crews easily and take your time and stun every enemy in many a fight, so it's not uncommon to bag more than the capacity of a single prison in prisoners (for enslavement) especially if you have a few VIPs or something lingering. The "prison is full" screen doesn't allow you to transfer prisoners elsewhere, just to ransom them, so if you bagged too many, you have to ransom a few (a waste of loot and slaves). That is, unless you exit the game and reload from the post-battle autosave, which nicely saves before you have to deal with prisoners, allowing you to overfill the prison. Yes, I've done that before because I don't feel guilty when cheating a mechanic that makes no sense: In this case prisons having a hard cap and not being able to temporarily guard a few extra prisoners or at least transfer them to other bases on the spot.
TL;DR: Having the opportunity to get a prison with larger capacity in the end game would be convenient, allowing you to save base tiles by spending money. I'd certainly use it.