I thought that didn't affect /system and therefore the gapps would be restored anyway...I also had this problem last month. I went to the advanced wipe menu in twrp, and in addition to the usual wipe options I did a "factory reset". I guess there are probably better solutions.
In any case I solved it by modifying the /install/bin/backuptool.sh script inside the LineageOS rom zip. I added a "return 1" as the first line of the check_prereq() function to avoid any backup/restore and flashed the modified zip. All good. That disables ALL backup/restore scripts, but the only other script in /system/addon.d/ is for backing up and restoring /etc/hosts, which I don't touch, so no problem.