Yes, although it would require a lot of work, you can technically do that with FEATool Multiphysics (but not CFDTool as it doesn't support scripting).
As all FEATool models can be exported and run as standard Matlab m-file scripts, you can also write your own interfaces around it using the Matlab UI controls. The functions available in the public user facing API are listed in the following link
https://www.featool.com/doc/files.htmlbut the easiest/most convenient way to learn is basically to use the "File" > "Save model as M-file script..." menu option and go from there. For example, the user "randress" built a custom GUI for slicing/splitting geometries:
http://forum.featool.com/Scripts-functions-to-split-cut-model-with-an-axis-orthogonal-plane-td666.html#a667A custom GUI toolkit was also built for the FEATool GUI
https://github.com/precise-simulation/guitoolNote that if you build a custom GUI for a simulation model, users of your custom interface will also need a license for FEATool to be able to run it.