... a vacation will make you more productive because you come back feeling more motivated and ready to work harder.
You are correct in believing that the 'default' interpretation of this sentence is what some grammarians call generic or habitual: it expresses a general truth about the consequences of taking a vacation, not a prediction about a specific instance.
In this case will does not express future reference but tendency; it is the same generic/habitual will you have probably encountered in the past tense:
When we were children we would go swimming every day.
This interpretation is pinned down by the use of the simple present come in the subordinate clause. In fact, you could use simple present in the head clause, too, without changing the meaning:
... a vacation makes you more productive because you come back ...
Consequently there is no need to add always to reinforce this reading. (In fact, always may be more than you really want to say—it implies that people never come back from vacation exhausted from their activity and resentful of having to return to the daily grind!)
However, it is possible to use the same main clause, with will, to speak of a specific future instance; but that will require you to change the form of come. It is easy to imagine a context; suppose your boss is talking to you:
Jihoon, I insist you take a vacation next week. I know you're very busy now, and you're unwilling to let the work pile up. But you're tense and grumpy; you're making a lot of mistakes; and you're actually creating more work than you're performing. And I do think that in the long run, a vacation will make you more productive because you will come back feeling more motivated and ready to work harder.