Is it possible to build the GitHub code for linux with something else then Electron?
I have several problem with Electron and want to build it with another builder. How can I do this or can I even do this?

Building instructions are on GitHub;

You would want to modify Electron.hx to pull each respective API from new source.

If you don't (e.g. just run index.html on a web server), GMEdit will work in "lite" mode where it only loads a pre-defined set of plugins (see PluginManager) and opens/saves project ZIPs or YYZs.

Since you did not identify the specific problems nor what you want to use as a replacement, that's all I have.