The web store can only distribute one version of your extension. If you set the minimum Chrome version to 88, then users running any previous browser version won't be able to install or update your extension.
MV3 is still quite buggy and incomplete, so it's not a good time to update your extension to MV3 yet.
It's better if you publish a separate extension as an MV3 beta and keep the MV2 version as the official/stable version.