Bounty reputation is removed when the bounty is offered, not when it is awarded. Basically the user has offered more than half of their reputation as bounty for that Q&A.
From my own reputation activity page when I've offered a bounty:
Yet the bounty wasn't awarded until a week later. This is the reputation activity from the user who earned the bounty....
Modification to how bounties work is not something that we at GIS SE can customize at a site level.
Consequently, you would need to post such a feature request at Meta Stack Exchange which deals with network-wide issues.
If you decide to post there be sure to look for any duplicates first because the site is quite unforgiving on anything tagged feature ...
Implementing an enhancement request like this is something that could only be done at the Stack Exchange network level i.e. via Meta Stack Exchange rather than here at Meta GIS Stack Exchange.
I could not find a similar request there when I looked just now but if you decide to post there then, before doing that, be sure to review How does the bounty system ...
As commented by @Aaron:
There is an option to include a message in the bounty, which will be
displayed prominently with the bounty.
In this case the message written by the person placing the bounty was:
Offering a bounty to refresh this question to current day. Also to
encourage people to flesh out how to use [conda] and it's packages if
you've installed ...
Normally, I would say, without hesitation, that you should edit your question in such a way that it does not unduly invalidate any of the existing answers (or touch up those answers at the same time to keep them "in sync"), and consider adding a bounty, in order to draw new attention to it.
This would be in line with Getting attention for unanswered ...
I think it is too broad too.
My feeling is that multi-part questions are not in the spirit of bounties (nor the site in general), and irrespective of the bounty I think it should be closed.
I have determined that the bounty can be refunded by moderators, which I have done, so that this question can be placed On Hold pending the question being further ...