Yes, you can modify idioms, but no, go on bare foot sounds strange. It sounds like you meant to say go barefoot but made a mistake.
Usually when we modify an idiom, it is to make a little joke. The listener is expected to understand the idiom and the variation from it. The humor comes from the difference. You somehow make an analogy between part of the idiom and the present situation. For example:
Are you quitting smoking cold turkey?
No, I'm, uh, quitting "warm turkey". My last cigarette is scheduled for next Sunday.
It looks like Janet here has a sweet tooth—and a sweet nose, too. [Said just after Janet got some chocolate ice cream on her nose.]
There is no rule for when this will be successful, of course. Modifying idioms is creative, figurative language. Doing it well requires familiarity with the style in which new expressions are created in English, or how far you can stretch conventional usage and still have people see it as deliberate rather than a mistake. That takes an even longer time to learn than the basic grammar.
Walk with your bare feet and go with your bare feet also sound strange, though not as strange as go on bare foot. They could be used for emphasis or to direct your listener's attention in a different way than go barefoot, as in "Walk with your bare feet on the ground so you feel the grass."
Of course, just because modifying idioms is hard to learn doesn't mean you shouldn't try. But expect that it will be frustrating. Opportunities to do it successfully are rare and a fluent speaker's ear is needed to tell if you were successful.