A couple more thoughts on making the Pershing plot tie a bit more into a solid movie surrounding the season finale content:

The moment in the Pershing storyline where it’s mentioned that Gideon never made it to Coruscant for trial could lead nicely into Carson’s discovery of his shuttle, bringing him back into the fray and further emphasising the link.
Then, the Shadow Council scene could return here a few scenes later. If we emphasise the link Pershing > Carson > Gideon (which’ll supplement the existing Pershing > Kane > Gideon link), that’ll further allow the Pershing content to feel like setup for the Gideon (and thus Mandalore) plot.
I know you like the Shadow Council scene where it is - and it is genuinely good there - but this might be better value for money. (Or perhaps it can be split in two, with the state of the empire in the earlier movie, and the requisitions part in this one).
You might also be able to transition from the end of the Pershing storyline to a wide shot of the Gideon clones (maybe also the close shot of the one opening his eyes), to tell the audience ‘oh shit Gideon has clones’ before the Mandalorians find out. Then, when Mando discovers and destroys them, it’s a bit more of a thing than simply discovering and destroying them in one scene. Then, Gideon’s after-the-fact monologue about how angry he is that his clones died will feel a bit more relevant as we the audience have spent more time on that plotline.