I don't have an issue with the starters being forced in these dungeons. I have an issue with an extra member or two not being allowed. Plus, little Timmy would bring his starters to everything, because little TImmy's starters would be stronger than anything else they have, due to gummis and statboosters likely being allocated to his starters, as well as exp being maximized to said starters. The only people ditching their starters after graduation are playing the game in a hyper specific/weird way, which is in a lot of ways counter intuitive to the eventual endgame story dungeons being decent spikes even in vanilla. "Benced" also implies that you're never using your starters forever. Maybe a player will still bring them along but not as leader? Options options.
Another issue comes into play with the story around the dungeons that are suddenly restrictive. These dungeons are softer on story. They aren't Hidden Land or Dark Crater by ANY stretch in terms of story involvement. They are in between quests that have dialogue from other characters. The dungeons with direct story involvement from the starters perfectly fit into the starters only mold. However, everything in between Mystifying Forest and the Darkrai/Cresselia arc offered minimal dialogue from your starters. The Manaphy dialogue is clearly "let's go to Miracle Sea" and not "just you and me go to Miracle Sea". It can be immersion breaking from another viewpoint, as an exploration into unexplored areas wouldn't just be a duo exploration.
I think that preventing players from using other team members that they potentially invested into is something that really neuters the fun of the in between post game dungeons. An argument can be made about game balance, however other party members will just be complete liabilities unless they have been invested into. It's better here than in the vanilla game, but they're still weaker than your starters objectively, due to exp and gummi acquisition. This is especially the case if you were to add party members later on in your journey, as they'll get less gummis especially if you're avoiding grinding missions. Less gummis will also mean them getting exp elite later, if available as a skill.
Should've been a toggle instead of a forced mechanic. Or better yet...let players decide. If a player doesn't give a crap about a third or fourth member...then they play that way. If a player wants a full stack for dungeons that aren't super plot focused, then let them. Forget "considering the options available to all starters". How about "considering the optional available to all Pokemon you've recruited"? Railroading players after giving them newfound quality of life and freedom = bad.