Flowey will mistake Frisk for Chara since their second meeting after toriel battle. It does not matter in what route you are on. Chara just needed to die and ask asgore to use their soul when they did. The whole elaborate plan to break the barrier and go out to kill more humans, forcing their friend to kill, imediately picking his body and going away, not even surprised by being able to control Asriel, make it seem like there was more than just freeing the monsters, that Chara had more plans.

I don’t think Asgore had any intention of ever taking Chara’s soul, because on Chara’s premature death bed he says:

Asgore implores Chara to stay determined and because they are the future of humans and monsters, and that they need to be alive in order to realize that future.

Asgore’s dream at this point is not just to free his people but for peace to be achieved between humans and monsters once more, and that Chara can be the fulfillment of that wish. But for Asgore, Chara needs to be alive in order to realize that dream.

So no, Chara asking Asgore to take their Soul upon death would not be an option.

Also, both Chara and Asriel were planning to cross the barrier and take the six needed Souls together. Chara may have initiated the plan but Asriel had been assuring them that he would not doubt them.

And even while Chara was comatose and not pressuring Asriel into following the plan Asriel continues to claim to be keeping his faith in Chara.

While both Chara and Asriel were going forward with this plan without any absolute knowledge of how Soul fusion worked, they were both still sure of one thing: that they were going to “do it together.”

We’ll be strong!

We’ll free everyone.

We just have to get six…

And we’ll do it together, right?

Asriel’s words suggest that while Chara would have just been a Soul after they died that they were still going to have enough presence to be able to act along side him.

While neither child knew what the logistics of the fusion would be, they still knew that whatever they did it would have to be done together, not divided, or with one exerting control over the other.

Asriel had just as much control over the fusion as Chara did.

There was nothing Chara could do without Asriels consent and vice versa.

Chara could not have “more plans” because for those plans to work they would have needed Asriel’s “okay.”

There was only the plan, and Asriel backed out of it when he realized at the last minute what the long term effects of that plan would have caused.

Which was good because it prevented another war breaking out between monsters and humans, but not perfect because it brought about both Asriel and Chara’s deaths and prolonged the monster’s entrapment and hopelessness.