Baseline:
When you use the hourglass and the war map, you are not opting in to a totally fair 1v1 crew vs crew fight. Nobody should be under that impression, Rare was clear about their intent to have adventure still matter in full.
You are opting in to having your ship relocated near another ship, to save you the time and effort of having to find targets manually, while remaining fully subject to anything and everything adventure offers. Including the other 4 ships on the server.
The provision of sbmm and ship-matching, which is a good thing, is an added bonus, given to increase the occurance of "real" fights and decrease the prevalance of one sided roflstomps, but while still fully allowing for both.
As for "fair"?
Well you could argue that because everybody has the same ability to do a given thing, it's automatically fair for it to be done. The same logic for saying a fight between a ship with only spawning supplies vs a ship with stacked supplies is fair, could be applied for outnumbering opponents.
But I don't like that manner of logic. I don't use "they could have done it too, they also had the option" as justification for regarding things as fair.
So I still call the spawn-supply vs stack-supply fight unfair, and I still call a fight where a ship is outnumbered unfair.
But something being unfair doesn't automatically make it bad or unallowable; not by itself.
This game isn't about fair fights. Unfairness is an inherent and intended component of the game. Unfairness is allowable and justified.
Fighting people with more supplies than you, people attacking your unmanned ship when you're in a cave/vault, tuckers waiting on your ship with a keg for you to touch the shrine loot mermaid, crews that found tons of curseballs vs crews that never found any, being outnumbered, etc.. All unfair, all allowable.
All else aside, any changes meant to target actual alliance servers, would also affect organic alliances and possibly even incidentally placed people, and therefor shouldn't be done. The Red Sea idea is especially bad, for what should be obvious reasons.
Personal anecdote: So far in every instance I've seen of faction war ships being outnumbered, it was the defender that was outnumbered. Yes, I've seen people tell the stories of people invading into alliances, but I've only witnessed defender ships get invaded the same time an on-server ship attacked.