I tend to like to ask about those in comments. I think often those sorts of answers are really useful because they answer a question that the OP didn't even know to ask. Other times, the OP is already far enough along in a project that they just have to say "it is what it is," and nothing but an answer to the question they asked is useful.
For example, if someone is asking about how to make some detail work out in a science fiction system which tries to game the conservation of energy law along the way, it may be very helpful to point out that not only does their system not work in our universe, but by Nother's theorem the entire class of systems they were looking at cannot work without huge consequences. It's also great for tackling mathematical problems where the problem statement is already inconsistent. It helps them not need to look in places that we know will already fail. It's easy to spin your wheels on a thousand ideas that don't work before you come across a simple clean proof that that entire chain of ideas must always fail.
For an alternative, When will uploaded minds be a reality, I have reason to believe some of the premises regarding how the technology progresses should be called into question. However, when I asked in the comments, JDługosz said such an answer wouldn't be too helpful for the story he was already writing (but it might be an interesting future question if we could ever formulate it in a not-too-broad wording)
The one real disadvantage to these sorts of answers is that they rob one of the opportunity for creativity and imagination. An answer along these lines basically says "Let me show you why my way of thinking is the only right way." In a lot of cases this is useful, but many worlds don't have to be quite as consistent as the reality we live in. If I went to two boys playing with sticks, pretending they were swords, whipped out a blade of my own and cut one in half commenting, "sticks can never be swords because they're not made of metal," I've ruined two boy's game... and what for? For all I know one boy may watch the way the sticks bend and sway and grow up to invent a new approach to composite materials because of those sticks. I may have cut genius short.
I haven't figured out the right way to judge which questions are the correct ones to raise issues about premises and which ones are not. I admit I tend to err on the side of cutting down faulty premises.