You would know more than I on the details of the domestic teams, but certainly in results and from what I've seen in watching Super Formula properly the last two years or so is that Mugen doesn't seem to be in too great a position now. You're right that the form of the teams does fluctuate somewhat, TOM's don't look as imperious in Super Formula as they have done before, Dandelion has got stronger in recent seasons up to now seemingly being near unbeatable in combination with Yamamoto, but I can't help but think that Ticktum had been put in a difficult position somewhat with the team he has been assigned to in SF and where they are in the pecking order right now.
It could be that at this very point Mugen may not be up to it yet relatively in understanding this brand new chassis, but M-TEC (Mugen) is the supplier commissioned by Honda to provide all the machinery (car, engine, parts) and services to all Honda teams (including themselves in Mugen) in SF and SGT, also manufactures custom parts for Honda's commercial cars, so M-TEC = Mugen is tech company while other teams are just racing team to receive and run the cars. So of all the possibilities lack of resource is least likely or quite impossible. They had been fielding only one car before Gasly, but actually that's because they themselves are provider. When Gasly entered in 2017 they expanded to run two cars, Gasly immediately delivered (while it took 3 rounds for him to be up there) and annihilated his teammate (Yamamoto).
Again for sure it could be Mugen is not in good state, for now for short/temp term yeah, but in longer term no, they have always been Honda's front team and will always be. If you race in SF for Honda, Mugen is always the first definite team you might want to join, followed by Dandelion. But you cannot always expect to be in the team when they are on top/usual form, also again it's not like he has been totally hopeless so you cannot judge anything unless you fulfill one season at least. He might start to deliver from round 4 or 5 like Gasly/Vandoorne/etc did, who knows. So for me it looks strange and brutal even for Red Bull standard to drop him like this, but I dont know, it could really be performance reason, or attitude reason like generally said (seems quite a few fellow Brits fans see issues in his character/attitude, but something like that is hard to judge for me when you are not the same nationality).