This is going to be hugely ESID, you have to remember, JET Program just gets you to Japan, after that, you are employed by your contracting organization, each one has it's own rules and protocol, and it's possible the JET in next town over will face a completely different set of rules than you.
If you're not married or engaged, it will probably be difficult to get permission for your partner to move into your CO-provided apartment. If you went and got your own apartment, I don't think the BOE can really forbid your partner from moving in, but getting your own apartment can be a huge hassle and your CO is under no obligation to help out. You may also get some shoebox Leopalace-type apartment where it's not feasible (and maybe not even allowed) for 2 people to live there.
That said, I'm sure there's plenty of stories of JETs who had their significant others move into their CO-provided places with little to no trouble. One JET in my prefecture lived with her non-JET fiance, and I knew a pair of JETs in a couples placement who weren't even engaged.
But japanagram, it's good to hear you're okay if you and your partner live apart, and as you said, it gives both of you the chance to experience Japan in your own way.