The first line in the sqlite3 article caught my attention. The user doesn't know this, but the impact described, remains.
In the gravity database, the table domainlist has AUTOINCREMENT, as far as I know there is no option to remove entries from this table, order will thus never change. The domainlist table is by far the largest table in the database (depending on the number of lists). reducing the resouces used, by removing the AUTOINCREMENT keyword, would make a gravity update faster (again, according to the first line of the article).
Not an essential change, but I remember this discussion, some changes can be made without major problems, there is always room for improvement.
Somebody in your team recently suggested to introduce certain improvements for new installations only, could be an option, although, the gravity database is recreated every time pihole -g is executed.
I also checked the pihole-FTL database, there are two tables with AUTOINCREMENT, messages and query_storage. I assume the use of AUTOINCREMENT in these tables is justified, because the user (messages) and FTL (query_storage) do delete entries, the order would be impacted by simply removing the keyword.