Would "well done" also apply to a presently proceeding action?

I think of "Well done!" as referring to a completed action. For actions which are currently in progress, you could use:

Good work!

or

Good job!

Using the past-tense word done indicates the task is complete. This sits in contrast to the present-progressive form are doing that indicates the task is still ongoing.

If I were the son in this scenario, as soon as my dad said "Well done," I would have stopped jumping.

The dad could say "You've been going for on minute. Well done. You are doing really well!" This would indicate that the interim goal of going for one minute had been reached.