The tough part with analogies like this is there are obviously rationals too large for any computer in the universe as well and anything which fixes that portion goes back to needing to reckon about the different types of infinities involved in the original problem.
I don't think that's the case here unless you are referring to a busy beaver thing I don't understand :)
If you are referring to the observable universe being finite, then that's not relevant for the discussion: I am just putting a few more grounded terms on the theorem that computable reals (including rationals) are a countable set. The point is that "for every integer n you can get n+1" is unphysical, yet "grokkable" symbolically, so it works well within a conceptual mathematical universe (regardless of what the physical universe has to say about it). Within this math universe we build an abstract computer that can hold an arbitrary rational/computable number, but only a countable subset of the real numbers, since almost all real numbers cannot be described by any "physical" program, even if that program is larger than the entire universe.
I wish I understood the busy beaver problem / connections to Ramsey theory / etc. However for this intuitive discussion it seems like a serious digression.
This is what I mean in that it only appears more grounded if you already understand why a countable set has a different type of infinity than an uncountable set in the first place and what type of universe that implies. Otherwise you're left wondering what type of universe is needed and why it is that type of universe can account for some infinities but not others. The latter part is just the answer to the original question of what the difference between a countable and uncountable set is again so if you can answer that you didn't have the question to start with!
I think you are getting away from the actual original question, which is why (intuitively) the rationals are dense in the reals despite being a different form of infinity. The confusion wasn't about different forms of infinity, it was really about the topology of R with respect to Q - why is Q "big enough" yet Z "too small" despite the sets having the same cardinality? And that is intimately related to any fixed real number having a computable/rational approximation up to any accuracy, yet most real numbers not actually being computable.
