Every month or two, disable the overlay (again using raspi-config), reboot, apply updates, re-enable the overlay, and you are good to go.
Also, if you are using a PI4, switch to booting from a USB stick and just forget about the SDcard.
(I've been running openwrt on a pi just because it had an overlay filesystem - I could run raspbian now)
Never had trouble with the 3 that was a Kodi box and latterly has been used for some electronics experiments, the 4 that is my current Kodi box, or the 400 that has been playing as router+firewall+VPN since early this year (at the time getting a 3 or 4 for the job would have been either expensive or near impossible, and I didn't want to try a potentially less well supported option, but I spotted a nice offer on a 400).
(I'm not blaming you, it's hard to have a pure RO FS, that would help a lot - and a standalone RPi doesn't need a lot of stuff that comes by default)
I have /var/log and /var/tmp on tmpfs tho
And I don't need much, just 32MB would be enough, I would just boot linux using using a read only SD card.
It's a major flaw, I don't understand why they did not find a fix yet.
It boots in about 10s now too.