There are several ways to create such an effect, but I only explain one here. There are also easier solutions for the problem, but this method influences other functions less.
First, you modify the final boss characters so you can transform into them. Then add a characteristic itr/kind: 0 in the standing, walking, running, jump_attack, defend, and jump frames of the characters who should influence the appearance of the final boss\.
Now in stage.dat you activate a criminal which can be hurt by these characteristic itr's and will go to different frames depending on which one it gets hit by (use bdy/kind: 10xx). In these frames, the criminal beams to another enemy character activated in stage.dat (in the example it's template) and catch it with itr/kind: 3. The itr/kind: 3 brings template to different frames where it transforms into different final bosses.
Right now it sounds really difficult - but actually it's quite an easy system, but if you have a lot of characters which should influence the final boss you'll have to do a lot of coding, so maybe you should combine this with the Stage Lock system.

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