The 3 months guidance for the visa start date doesn't have anything to do with the 12 weeks processing time, as far as I know - since it applies to ALL visa types, not just spousal visas.
The 3 months starts from the date you submit the online application, not the date they start processing the visa. It should be stated on the information page for each visa type on the UKVI website.
It has always been 3 months ahead of your official application date (the date you pay for the visa), regardless of processing times, but it's just your intended travel date - the visa doesn't have to have been issued by that date by any means.
[Similarly. for US non-immigrant visas, you can't apply more than 4 months ahead, but the actual application only usually take a few days to be processed and is often issued same day, at the interview.]
We have seen UK visas refused in the past because the travel date indicated on the form was more than 3 months ahead of the official online application date.
Not sure if it is still the case but the online form didn't used to allow you to put an intended travel date of more than 3 months ahead of the date you submitted the form.
This year is completely unprecedented in terms of visa application processing times. In the past it has never taken more than 2 weeks to receive the first email for the processing to start... and this year some people have had to wait 2 months for it.
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