If your ME Non-B is still in date/valid on your return from Europe to Thailand you will get a new 90 day stamp. If your Visa expires when in Europe then purchase a single entry re-entry permit to keep your current 90 day status live on your return.
Thai partner means not wife (I assume) otherwise your solution would be easy, a Non-O marriage Visa giving you 90 days on entry followed by a 60 day "Visit Thai Family" extension.
The timings you lay out work as you say, only just, but what you do not mention is the possibility of a house visit during the under consideration period when the person applying will be out of the country on the
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working cycle. Should the application not be submitted on one of the 28 day cycles when in the country notifying Immigration of the departure flight on day 28 of the current entry stamp?
You get stamped into Thailand with the Non-O Visa which allows you to open a bank account and transfer the funds to season in time for the extension application, that's how
You cannot use the 65k per month method for a retirement Non-O Visa obtained in Thailand or for the first 12 month Extension of Stay unless your Embassy still does the income affidavit (USA, UK, Australia etc. do not).