The simplest solution is to keep your source in the root of the plugin folder (i.e. your typical WordPress setup listed above). Your build script should write its output to a dist folder at the root of the plugin.
This prevents any possible WordPress conflicts; PHP and WordPress won’t parse a file unless it is referenced with an include, require or otherwise in your code. So my_plugin.php in the root of the plugin and in the dist folder won’t conflict at all.
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