MuseScore4 taking over MuseScore3 files

I've got scores dating back to the Summer of 2011 (v 1.2), through 2.x, 3x, 4.1.1 and none have been converted, reformatted or otherwise changed except for the ones that I opened in 4.x and then saved with the original filename. When you click on a file it may open in MS4 if your operating system has that file type associated with MS4 but MuseScore won't go hunting down your files and open and change them on its own.

You started wrong.
All Musescore major versions create their own folder (MuseScore3, MuseScore4) in the Documents folder (Windows). And both have a subfolder called 'Scores'. After installing a new version, the mscz files are associated with the new version when you try to open them with a double click in the file manager. This is caused by Windows.

If you are upgrading to a newer version, it is a good idea to copy the MuS3 scores to the MuS4 scores first!
Then you can open the scores from the MuS4 folder and save them in the new format, but you still have the original MuS3 scores as backup and to work with them in MuS3.
If you want to open a file from the version 3 score folder with MuS 3, you should open MuS 3 and use File/Open there and navigate to your score. Or you can right click on the file and select "Open with" and then MuS 3.

If you have already overwritten your MuS 3 scores with the MuS 4 format: Open them in MuS 4 and export them to XML. Move them into the MuS 3 score folder. They can then be opened in MuS 3 and saved in mscz format.

I can't use MuS 4, so I'm not sure what problems might persist. I have noticed an incompatibility if you used the masure repeat sign and the title block may be unformatted. Also, some characters (segno, coda) may be smaller.
But I extracted the mscx file of a MuS4 score by unzipping the mscz, so the incompatibilities may not be present via the XML export. I don't know this.

"Can I do anything to change this situation?"

Sure, you can tell your OS (operating system: Windows, macOS, Linux) to open .mscz files in MuseScore 3 by default.

Because I still do all my serious work in MS 3.6.2, this is how my Windows laptop is set up. All .mscz files open in MS 3.6.2 unless I really need to use MS 4. If I do need to open a score in MS 4, then I have to tell Windows specifically by a right-click: Open with > Choose another app > MuseScore 4

And please take the advice above from @underquark and @HildeK: keep your MS3 scores and your MS4 scores rigorously separated in their default Scores folders.