Wix data Store / Variants limit (And impossible to bypass ?)

No. Unfortunately, there is no way to have a job lasting more than a minute or so (not even a warranty).

Another way is to have your cron job host on another service and call each page from your other service with a longer timeout (but you still need the pagination)

If you want to do a loop, you need to loop over all items, flag each item as processed somehow (in a sync database). Then on your next cron batch, process all items that have not been flagged yet and restart.