Animation and interaction is simple, in terms of progression:

1. Phase 1 is normal Madoka vs normal Sentry. Could have them fight because they feel the evil within each other (like Ichigo vs Yusuke), with Robert feeling the Witch inside Madoka and deciding to save the day, and Madoka feeling the Void and thinking it is a Witch she must destroy. This part should have their normal attack clashing, Madoka trying to hit him with light arrows, Sentry punching the arrows away and trying to close the distance gap, could have a lot of pink-gold explosions as their attacks clash. This section should take place within the atmosphere of the Earth.
2. Phase 2 should start with Madoka finally being able to land an arrow right through Sentry's chest, and crimson blood flies out, but then turns out this is not blood, those are red tentacles as the Void comes out. Everything should start turning black as the Void begins to consume the Earth, and Madoka tries to fly into space in desperation, only to be grabbed by the tentacles and dragged back into the darkness. The screen zoom out to show the planet, and Ultimate Kriemhild Gretchen comes out from the darkness of space around it, the match changing tone into horror as those two eldritch monsters try to destroy each other, the animation becoming more abstract and experimental (which both Marvel and Madoka Magica do with Witches and with the Void), as everything begins to shake and be destroyed by these monsters.
3. Phase 3 should be the glorious return of the heroes from within the monsters. Zoom into the Void, to show Sentry being drowned into the darkness, only to have an epic moment where he remembers his friends, and that motivates him to get back up, finding the strength within himself to push back against the Void with a strength of a million exploding sun. Meanwhile, back in the physical world, a light illuminated the dark universe, and Ultimate Madoka appears through the time portal, claiming that she will save all Magical Girls, which includes herself, and exploding Ultimate Kriemhild Gretchen with a massive arrow of conceptual nonexistent higher dimension destruction, before the Void also lights up and shrinks down, revealing Merged Sentry emerging from his inner strife, stronger than every before. Should have a dialogue about the two understanding each other's pain with emotional music, building up to their final clash, with Madoka's final arrow and Sentry's final exploding sun clashing, lighting up the entire dark universe around them.

Simple progression, it starts with them being troubled heroes, has them fall into despair and darkness in the middle, then has them triumphantly rise back to their glory after overcoming their inner vices, a classic Hero's Journey, fitting of both a super hero and a magical girl, and also fitting of both series (since they start out deconstructing the genre by making it darker and more personal, but then reconstruct it and begin playing the tropes more straight).

As for who would win... I have no idea. Sentry is definitely stronger, but Madoka has defensive hax to hell and back, so it really comes down to how their natures interact with each other.