Just a couple of thoughts.
Losing immediate functionality
If you’re not storing the propriety format you are losing important functionality.
As annoying as proprietary formats are, they store the metadata in way that is compatible with the acquisition equipment.
This allows users to return to microscope and easily replicate the setup from the file. This is not possible if the file had been converted.
There is no universal format
Each file format organises the metadata is a way that is convenient for that instrument. This is the schema and it reflects how the manufactures choose to conceptualize the imaging process.
For example, think about describing the filters on a fluoresce microscope. One maker might use filter cubes so it makes sense to group the beam splitter and emission and excitation filters into a single unit. Another may use filter wheels, and yet another may multiple beam splitters and emission filters going to multiple cameras.
A common file format is going to have to employ a mega-schema that can describe all these situations, whilst the manufactures use a minimal one that suits the equipment.
Working with the mega-scheme is cumbersome as it will be full of details that are irrelevant most of the time. And as pointed out above, maintaining the mappings to the mega scheme is a Sisyphean task and there will always be parts missed.
Maintain a computer environment to translate the file
Rather than keeping the original and a converted one, you could think about keeping the original file and maintaining an environment that can translate it.
I think it should be possible to setup a virtual machine or container that runs a program (bioformats / imageJ) to convert the raw image. We have virtual machines to run windows XP software that are well over 10 years old.
The other advantage is that as bioformats improves with time less data is lost at the conversion stage. This is pretty much how OMERO works.