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Not always the same. Compare some situations:

1. Someone is waiting for you outside near your home. He just wants to have a talk with you. And he does not ask for a permission to enter. But you...

Yes, I would say it makes sense considering the scenario as you described it.
In this situation, you use "войдите" when someone is already about to enter waiting for you to open the door for him....

Actually, it is a hard question to answer just because either verb has multiple meanings. And they partially intersect.

Antonio, could you provide a context to make it easier to explain?
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