Only using your examples and keeping the definitions very narrow because @Stephie is completely right:
To end means to finish or complete something.
To end up means to to become something.
"I want this to end." means the speaker wants whatever action is occuring to stop.
"I want to end up like Michael Jordan." Means I want to become something (a skilled sportsman, or famous, or wealthly) like Michael Jordan already is.
To help means to give assistance or to join with others to complete a task.
To help out is, for all intent and purpose, identical to
To miss means to fail to achieve a goal or expectation, or to fail to arrive at an expected destination.
To miss out means to lose (miss) an opportunity.
How a phrasal verb relates to the original verb has more to do with the culture that caused its creation than any rule. My favorite comes from the 1970's.
A freak is someone or something unusual or abnormal.
To freak is to act unusually or abnormally... except...
To freak out is to suddenly act abnormally or wildly.
The exception I noted is that it's become common in spoken English to use the verb
to freak as a short form of
to freak out. Because it's uncommon for a phrasal verb to be used before it's parent verb, this is likely an example of an original verb falling into disuse, then being picked up again for another purpose.
Living languages... you've gotta love them.