I use direct external boot from SSD with MMC as second boot option. It is a bit like extroot but without the big hassle with updates. Updates work like reboot to MMC and update there. Side effect of my solution: the led counts for recovery etc are off by one (1 LED boots to SSD, 2 LED boot to MMC (normal), 3 LED rollback snapshot on MMC, 4 LED factory reset, …). This will be changed back to original if i find a way to detect if reset was pressed but only for the first LED or not pressed at all.
This may break a bit when you disable extroot but flashing with the medkit (recovery) will work. Another option could be chroot to /rom (mounted r/w) and callling pkgupdate but there may be really nasty side-effects.