I like that "put the toys back in the box" analogy.
And you're right. With things like the parallel quests, they basically have free reign to do whatever they want with the timeline. It'd be nice to see PQ's take on a different role in future games. Instead of being quick one off what ifs to just add a bit of content, maybe flesh out miniature stories about alternate timelines that take place over a few missions.
I stole that off a marvel editor I think (Tom Brevoort?) who was basically using it as an excuse for why they can never really have any kind of progress or real change in the marvel universe.
Here it's 'justified' though as obviously a DB game isn't going to override the main manga/super canon.
We get discrepancies like purple/blue Trunks... Ideally they could co-ordinate and write around Toriyama and do canon stuff, but I think the idea is the primary doesn't want to be limited and restricted by being burdened with the need to coordinate with the secondary thing (XV)
XV1 did imply there are as many timelines as they wanted. Such as Percel saying he was working on one for a presumably long term basis.
At the time they had no reason to assume AT would have a problem with this and if anything it kept them out of trouble of interfering with the main timeline.
At first glance it would appear this whole canon thing with time rings showing the "final number" of universes (didn't they fuck up and miss out the 'unseen' timeline though?) has limited Xenoverse.
However we know all the "present day" stuff from XV1 and 2 is, relatively speaking, in the future of the canon timeline.
So actually it's ok because you shouldn't expect Percels timelines corresponding ring to be in the box in DB super, because it hasn't been made yet.
The parallel quests are IIRC currently described as being little fragments of timelines that aren't real. This is sort of a hand-wavy justification for being able to erase them and effectively kill/erase anyone within. They hurt the timeline just by existing, perhaps they go away on their own slowly but it's best to get rid of them and make sure too many don't build up. They are the plaque on the teeth of time and you are the brush.
In reality the fluff about PQ's is really just a game play vs story hand-wave and it's best not to thing about it or the individual events being canon. Just have the vague idea that You and sometimes your mentor erased tiny superfluous time fragments in addition to your main duties.
I really wish someone would make a graphic/guide for all the universes and timelines and the different faction in them, color coded for it's source (what level of canon it is).
[But I know that super autisimy of me]
What I've always said, ask Toriyama for *one* canon timeline he isn't going to use again and let them really go crazy with that, or a new one. But they are overly cautious and as a result it's not fully running at it's story telling potential IMO.