(Quote abbrievated for brevity.)
This is the expected behaviour. pyproject.toml makes pip enter build isolation mode; pip would populate a new environment with the specified packages, separated from the runtime one, for better build reproducibility regardless of pre-existing package installations.
The best solution at the moment is probably supplying --no-use-pep517 to pip can stick to your development workflow prior to the pyproject.toml addition. PEP 517 is still missing a lot of pieces, especially those related to development and debug workflows. I believe there are some work to amend this, but the progress is slow due to resource constraints (see Specification of editable installation - #40 by pganssle).
Cc-ing some people that might be interested in this topic (from the mentioned thread): @pganssle @pradyunsg @techalchemy