As far as python and pip is concerned, I think pkgsrc should contain only python packages which depend on non-python ones already available. The packages which are easily to install using pip should be used with venv, which to my knowledge is the recommended python development method anyway and will not mess with foreign files present in the pkg tree. This approach can help minimise the number of py- packages in pkgsrc. I am not sure about how npm works, whether there is an equivalent to venv; as far as texlive, I only have used the meta packages for whatever needs I've had over the years.
I think something along these lines should be preferable - in the presence of a native package installer capable of working for an individual non-root user, to try to minimise the corresponding content in pkgsrc. The other day I tried to build py-matplotlib with the graphical interfaces with pkgsrc on an OpenSUSE Tumbleweed system, everything in the build went right, but at the end no graphic window appears when the test program is invoked... The native 'pip3 install matplotlib' worked of course.