I am not 100% sure. The evidence from my experience and what I have heard seems to suggest that they only count Penang issued visas. The worst case there is you must If you never had at least a SE non-immigrant visa from Penang, you may only get SE non-immigrant visa on the first application. so in 3-5 months, you would have to return to get ME non-immigrant visa. I guess if you live closer to the south or near bangkok (or near an airport/train), the train or air ride isn't too bad.
There was a report recently of someone with a new passport, but had copies of his 1st page (with photo and signature) and the last ME non-o visa from penang from old previous passport. So he was able to get ME non-o visa from penang on "first" application of his new passport.
I do have to admit though, these guys can be quite busy. So they might prioritize local customers first. Callers second. If these agents didn't exist at all, imagine you'd have to figure it all yourself with trial/error.
Thailand is not really the place for that attitude. And definitely not the Thai consulate. Just keep smiling and have the minimum documentation, you will be ok. Calmly make your case if any eyebrows are raised; and keep smiling.
At least you know you have some standing (at worst, SE non-o; or marriage and then Penang/Savannakhet). Consider those digital nomads and such that cannot get their back-to-back TVs anymore.
A third option might be to contact at Herbert at HDVisa (Koh Samui). Not sure if he will only discuss certain things in person. But he mainly deals with the Kota Bharu Thai Consulate. And he's been known to get things done according to a couple of sources. Whether he can still do it or not, you'd need to investigate. Especially since you "don't like surprises"