"many instruction videos and tools are designed for workstations"
(That should probably read: for home users)
A fair assumption for many home users would be that they don't make (regular) backups and their laptop/pc is their (only) pet. Their time and effort are "free" and their data and files have only become really valuable to them after that malware infection.
On that premise it makes sense that they expend significant effort into making a laptop or PC functional enough to properly boot and becoming useable enough again to access and recover their data and files.
For many home users in such a situation that is already quite the achievement and they're happy now.
End of video.
They either don't know or simply ignore that of course their system isn't "fully repaired" and that data still can't be trusted to be clean.
As a professional you might be getting directions from people that have the worldview of such a home user (i.e. that "repairing" and getting a compromised system back up and running is an almost insurmountable task and always necessary to recover files and data), who believe that you as professional can achieve many things they can't (admittedly correct) and who then (incorrectly) also believe that when YOU make the repairs the compromised system and data can be trusted to be clean again without a re-install.
It is up to the IT department / you to give proper pushback there.
For example in theory (and in reality, right?) you have proper back-ups and/or data replication to meet the RPO and RTO and don't need to recover data from a compromised server for business continuity.
Nuke the compromised system, run your automated installation and configuration scripts, redeploy and be happy.
I think my workflow would probably be something like:
Clean up machine/Recover files that has not been backed up
-> Nuke/reinstall machine
-> patch/update/restore backup
-> add machine back to the network.
It sounds like that you're starting to write what in "enterprise jargon" is called an Incident Response Plan.
That is a reasonable first start. PhilL W.'s answer already linked to a good resource here on ServerFault but please be aware that the incident response plan is not only written by and for a system administrator, but should also be supported by your business. The decisions there are closely related to your disaster recovery plan where often data backup and recovery (RPO and RTO) are decided.