"Is it OK to make it cheaper?"
This can be unnatural Chinese. Duolingo should be dialect agnostic and thus should not include the 儿 in this case. 便宜一点，行不行 is fine.
"Dialect agnostic" is great way to put it. I do agree that the 儿 should not be required, though a supplemental lesson on its uses in certain dialects would certainly help for reading comprehension.
It matters. 行不行 is equal to "OK?", so you can just imagine why it is not acceptable to say "OK? Make it cheaper."
I find this translation awkward and kind of weird. Without context it feels like you're talking making something for cheaper, when I think the goal is to ask can you sell something to me cheaper. A better english sentence would be "Can you do a little cheaper?"
I'd say ”Can we go a little cheaper?" to make it clear that we're haggling here. Otherwise we could be talking about making a product cheaper or something and it's a bit of an awkward sentence.