I have enjoyed my long distance with Thai from the UK. I have also flown EVA a couple times for short haul. I am ready to try them for long haul, I was impressed so much!
I think as long as you leave for more than a day or 2 (I would personally suggest a week), then you should be fine. You DO plan on getting extensions, right?
I personally would try a border run, not a bounce. Stay somewhere for a week. When you re-enter, make sure you have a departure flight. You will get more scrutiny for an almost expired passport. But they may let you in if they assume you are leaving within the 45 days.
Still trying to piece together how you got yourself in this mess.
Less hassle would be to come visa exempt for 45 days, and extend for 30. But if you are dead set on 90 days at a time, then you had better get on that visa now.
it may help if you stay in a hotel on occasion for a day or 2 on entry. I would think the same local non hotel address would raise flags as well. Just my thoughts. And maybe stay at a hotel for a night once a month?