from what I understand he used several shortcuts directly into nw.js and internal windows functions, and those shortcuts don't work on mobile and web.
most likely the shortcuts made programming easier for him, but they resulted in the known compatibility problems of his plugins.
never forget: most free plugins get programmed because their programmers need them for their own projects, and as a result they are not always compatible with game projects from other people.
and SRD appearently never cared for compatibility outside Windows.
The supertoolsengine specifically saves its changes to windows (size, position, # of columns, etc) in a windows.json file that it saves inside the data folder of your project.
On a windows deployment, it uses a filesystem request to find and read this file, if it exists. When you use web deployment, you can't access local files using the fs request, for security reasons. Mobile deployment (at least for android) is just a wrapper built around the web deployment, so it suffers the same problem.
This could be corrected if the changes to the windows were saved into a file that can normally be read by the engine, such as a plugin parameter, but the main reason they're saved in this way in the first place is so that the configuration window can access and modify these settings during playtest. You can't easily modify plugin parameters during a playtest, so he worked around this with the json file.
I'd suspect most of his plugins that have an editor window popup like supertoolsengine does have the same issue with mobile deployment. There isn't much you can do aside from ask him to make some sort of plugin command that 'bakes' the settings into a plugin parameter or something.