We're not aware of any such issues with the new Windows WebView2 exporter. If you run in to a problem, please file an issue.
False positives are common with antivirus tools and have historically affected any kind of executable. We've had false positives with NW.js before too. It's not really related to the kind of export.
NW.js had a range of bugs and issues that proved difficult to deal with - including many complaints about the file size of exports - and having two export options complicates supports and doubles the amount of maintenance work involved. As our newer export options now cover all the features previously supported by NW.js, the time has come to retire NW.js support and focus our efforts on the new ones.