The issues is rooted in render() of typo3/sysext/form/Classes/Domain/Renderer/FluidFormRenderer.php. Here the template paths are injected from the Yaml configuration.

As I agree that this is confusing I tried to see if we can either get rid of the TypoScript configuration or merge the pathes. The former will simply break ExtBase as the pathes are missing. The latter has also a problem. The renderer has at this point the resolved array of the pathes set by TypoScript. OTOH the Yaml pathes are yet to be resolved. So the pathes of Yaml could at this point either be put before or after the TypoScript pathes.

Solution 1:

Merge both TypoScript style arrays somehow. Either by processing the template path rendering options ouside of the Fluid form renderer or passing the relevant parts of the plugins configuration to the form renderer.

Solution 2:

Add a setting to the rendering options to either overwrite the TS pathes (current behaviour), to put the Yaml pathes before or after the TS pathes.

Solution 3:

Don't let the pathes be set by Yaml at all. After all this is TYPO3 not Neos. So stick to configuration style of TYPO3 which is (still) TypoScript.

Please stop to try to change this behavior.
I thought of something.
The most of the setting resides within a thing called prototype. Since a form definition has a reference to such a prototype, you can let the Frontend and the Backend parts behave different on a "per form" base. This is why we need the settings like template path within the configuration.
If you now try to move some things you destroy the concepts.
At this time, i write the docs. The docs will describe all this things and i will add some inline docs to the TypoScript configuration.

Patch set 2 for branch master of project Packages/TYPO3.CMS has been pushed to the review server.
It is available at https://review.typo3.org/52006