They may accept two accounts (ask your Immigration Office) but your biggest worry might be would BB do the paperwork for you having withdrawn the bulk of your funds?
To save time in Vietnam you can start to complete your application before you arrive then when you get your entry stamp upload that as proof of current location as soon as you get it and submit your application within minutes of arrival
There is a video link on the TM30 registration home page, watch that to see home simple the 3 step process is (after set up you only do step 3 in future)
Your Wise transaction should should have used the selection "Funds for long stay in Thailand" or words to that effect in the drop down menu for the reason for the transfer
The fact that you don't need a TM30 for a re-entry permit at the airport is probably due to the fact that you are in the process of leaving so your residence in Thailand has ceased/been suspended