Here is the cause of my problem.
So it seems to unsolvabel without hacks. Btw, I found a way to deal with it – my app is launched as a server, so it has system.d config (/ect/systemd/system/…) and in this config file I can specify needed env variables.
So, thank you so much for your time, your advice with ninja really helped – I use /etc/gstreamer/lib instead of multiply subproject paths, how it is done by gst-env.py.