I definetly do not believe the PCs should own a ship of their own. But just because its their base of operations, it doesnt mean it would necessarily be exclusively THEIR base alone.
Just.. You know, a friendly port run by other scoundrels you trust (or jointly owned in part by the PCs). Something of a Smuggler Coop. The sort of place you could stash some precious stuff, or lay low to avoid the heat.
Hell. That sort of communal group could take the form of an Obligation of its own. After all, they have to pitch in the ship's budget, or defense, etc.. At times.
It all depends on the scope of your campaign. Are you playing a game in which the PC's are trying to build their own smuggling/shipping operation ala Talon Karrde? Or is your game one where the PC's just barely surviving on the edges of space? Either game is a viable and fun campaign to run/play in, however in the first example, the PC's owning ship (or ships) isn't that unlikely, whereas in the latter example, it is highly unlikely for the PC's to own a ship beyond their starter as they are probably scraping just to keep it running.
He said in his first post, as well as the one you replied to, that he isn't intending for the PCs to own the large capship base.