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Digging a bit on the plugins that I could get my hands on, DotMovementSystem is one of (or the only) culprit, as it tries to pull its name dynamically (Source Code Protection has to patch MZ so it can load the bainry files that nwjs can read). It's fixable by changing the line 298:

const DotMoveSystemPluginName = document.currentScript ? decodeURIComponent(document.currentScript.src.match(/^.*\/(.+)\.js$/)[1]) : "DotMoveSystem";

To this:

const DotMoveSystemPluginName = "DotMoveSystem";

Might send a message to the dev of DotMovementSystem to let them know about it.

If you see similar issues with what you saw in that plugin, check if there any plugins that use document.currentScript (or similar) and simply change the line to hardcode the name.

As for Uncaught SyntaxError: Unexpected token '<': I can't say for certain what causes that on MZ. It doesn't crash MZ games (I tested with both barebones and more plugin heavy projects) and there's no crash or stuck in a loop. Most likely, there's a slight error in patching the html file so it can load the binary version of main.js. Other than that, it's a fluke of an error.

EDIT: If you mean the Source Code Protection on your edit: Yes. It's still an option. Since R6, it's enabled by default when the option to encrypt the assets is turned on. So, you'd need to disable that option first.