Great to hear! When it comes to ILR, however, and presuming the question "Have you ever outstayed your visa?" (or something along those lines) is on the application - what do you say?
You say NO, because you have not overstayed your visa.
UKVI specificallly states that as long as you have an application lodged and pending, you continue to maintain legal status in the UK (under the rules of the current visa) even if your visa expires while it is processing. You just have to get the application in BEFORE it expires.
The only situations where you would become an overstayer are if:
a) You didn't get your application in before your visa expired
or
b) your visa application was refused (and your previous visa had expired) and you didn't leave the country within the allowed time given after the refusal
A few years ago, FLR(M) applications were taking up to a year to be processed due to massive backlogs, and since a lot people can't apply for FLR(M) until 28 days before their previous visa expires, pretty much everyone who applied for FLR(M) that year ended up having their previous visa expire before their new FLR(M) was processed.