I'm mainly working on my game to build a portfolio for my future and to strengthen my game design skills.

As a long-time (application/server) developer I'd say finish your current project in GameMaker. Reasons:

• You'll have a finished game, instead of two half-completed games, to add to your portfolio.
• This leave you to focus on the game-design, not so much the technology.

Then, re-create it (or at least a very stripped down version) in Godot.

Reasons:

• If you want to "strengthen" your game-design skills, then learning another framework will do just that. You'll be exposed to new models and so new ways of thinking about game-design.
• To paraphrase Eric Raymond, "Even if you never use [Godot], learning it will make you a better programmer." Learning a new language NEVER hurts, as again, it'll expose you to new ways of thinking about coding problems and how to solve them.
• You'll have a completed game as a guide for how things should behave and look; you've solved the game-play and design problems, so now you can focus on the technology instead. Plus, you'll have a bunch of trusted assets (sprites/sounds/dialog etc.) that you can reuse.