I think that Pywikibot's save method should allow explicit overriding of a warning raised by abuse filter. It shouldn't be the default state, but it should be possible. Anyway, having a bot regulary hitting AF isn't a good idea - talk with an admin of your wiki.
On Czech Wikipedia, filters that would be hit by archivebot has exception, generally !"bot" in user_groups. This allows cs.wiki to warn users that may or may not know what is happening and allow bots to do their maintenance work without being warned because their operators are expected to know what is ok and what is not.