Jakub, "You will end up as your father" suggests that you will become your father. "You will end up like your father" means you will become similar to your father.
The sentence to translate was "Skončíš jako tvůj otec!". Is there a reason, why the posessive pronoun tvůj is used here rather than the reflexive possessive pronoun svůj? The subject of the sentence and the owner seem to refer to the same person ("you").
Here "jako tvůj otec" means "jako skončil tvůj otec"/"like your father ended up". In such a clause the subject/the originator of the action is the father, not the person we are warning.
I agree it's not necessary to include "tvůj", it's just usually included in this expression. Also depends on who says it. If your mother tells you this, she would likely omit "tvůj". If your friend does, he/she would likely include it, but not necessarily.