I understand the issues that go along with it. I liked the per-user interface that was set up, didn't find the interface clunky at all.
It does at least sort of favor pre-determined alliances, but... personally that's why I like the idea of limiting the point buy in or even making the point buy in for such games zero, so that these games are clearly friendly "variants" that don't effect the "main" games. However creating two "classes" of games (ie those that have point buy ins and those that don't) might be difficult from a site maintenance/programming. I can't really speak to that.
I don't really care about splitting the community, I think I, and most people would simply play in both types of games. They'd play some country-preference games, and some normal games. At least that's what I'd do.
As for it not being the best system for "trying out strategies" I agree, it's not ideal for that. If it were completely up to me, we'd have the choice to start games where everyone chose a power on a first come first serve basis or something, but I understand that's not practical, and that people would freak out about "pre-determined alliances" which I think I've already said I'd deal with by creating a "friendly game" category, with low or no point buy-ins enforced.
As for it being technically against the rules... I really probably couldn't care less about that. If it's fun, that's all I really care about. This isn't any kind of "official" tournament or anything, it's just a game. If we want to implement a house rule for some games, I don't really see how that's a problem, as long as it's fun. But that's just how I'd run things if everything were set up for my personal enjoyment, rather than for the enjoyment of lots of people.
All of that being said! You are the maintainer of this site, and are free to run it any way you want to. I understand you have a certain community you want to maintain here, and that's not only your right, but a very good reason to be very cautious about making changes. It's also why I'm very glad that you have set up the source-code to be open source, so that if someone else wants to set up another community, with a different feel and with different variations on the game they can! (So basically what I'm saying is I understand the difference between phpdiplomacy.net as a community and phpdip as a program/codebase, and that you have different priorities with running this specific site vs possible options for the game itself).