"at most" has the same meaning and would be fine here, but "only" has a different, more absolute meaning.
If we say the clock loses only a second....
we are saying that it definitely loses one second every 3000 years.
The other two tell us that the clock could lose up to (and not more than) one second in 3000 years.
It's a bit like saying, "A new car will cost no more than/at most $20000".
Clearly, that's different from, "A new car will cost only $20000".
buggles (not a teacher)
Student or Learner