Given that homos work perfectly until you save and load, and that same sex marriages don't seem to be saved any differently, it must be a problem with Tomodachi Life's save loading logic (Similar to X/Y's Lumiose City lock)People using the save editor for same sex marriages should expect some oddities, especially with housing. Having one only-female pair marry will result in a missing house (the game will act as if it is there, but won't be visible when viewing houses) whereas one only-male pair results in a house that crashes the game upon trying to access. What's strange is that the game handles them just fine upon marriage until you save and exit.
The game needs a sort of 'anchor' of the opposite sex in order for it to work. This can be done by either setting a gay and straight couple to live in the same house, or two gay couples (male pair and a female pair.) They create weird polygamy houses but they work relatively normally, though sometimes you'll only be able to see one pair or Mii in the house at a time, and one pair will take priority in showing up over the other. Don't be surprised if you catch a Mii hanging out or cooking with someone from the other pair, or worse, sleeping in the same bed...! I've also seen the occasional clone Mii show up talking to the original.
None of this is fault of the save editor itself of course, just a result of the game trying to figure out how to handle something unintended. Other than that, gay relationships actually work pretty well. They can still go on dates/propose/make babies etc. Props to the save editor for allowing it to be tested.
Sadly, it would take more debugging expertise than I currently have to figure out what these problems are.