As for your questions:
1. I don't see any mention of directory structures in PEP 503. The Morgan server does implement PEP 503 though. In any case, I tried installing now straight from the directory and it didn't work. Are you sure you meant PEP 503?
2. Where Morgan differs from pypickup, as I can see, is that it interprets requirement strings as per PEP 508 (e.g. "requests>=2.40.0; python_version < '3.8'") instead of providing a command such as `pypickup add requests`. For every requirement string, it looks for the latest version in PyPI that satisfies it, and downloads that version. You can filter _in_ the requirement strings, other than that Morgan doesn't have any specific handling of dev/rc/etc.
3. Morgan detects and downloads the build system based either on the [build-system] section of pyproject.toml, or the setup_requires.txt file (from setuptools). These are the sources currently supported. It doesn't actually care what the build system is, it simply attempts to find where it is defined and download it as well.
As for complex dependency specifications, yes, they are supported and honored (Morgan relies on the "packaging" library to properly evaluate those). By the way, I recently moved from Poetry to Hatch for managing the Morgan project itself specifically because I got fed up with Poetry not honoring those specifications, and trying to download completely irrelevant packages.