@Rob ********
as Lloyd said no issue at all applying for the multiple re-entry permit,
Just so you're clear you're not getting any "thai wife visa" you got a Non-O visa granted based on a Thai wife and now when you have 30 days or less left on that 90 day stamp you will apply for a YEARLY EXTENSION based on marriage to a thai at the immigration office for 1900baht
You'll get a 30 day under consideration stamp when you apply (and if you're traveling out/back in to the country during that month you need a new re-entry permit which is only good for that stamp)
THEN
when that 30 day stamp runs out you go back to get the year extension inked in
AND
after that you buy a multiple re-entry permit that will be valid the whole year and allow you out/in all you want during that time