Use ECDSA if you can, since it reduces the size of the handshake on the wire (keys are smaller). Don’t bake in intermediate certs unless you have a very good reason.

No idea why the RSA key worked even though the server used RSA — maybe check into the recent cross-signing shenanigans that Let’s Encrypt had to pull to extend support for very old Android versions.

I've been reading a little since then, and I think it worked with RSA root cert because this cert was a trust anchor of the Chain of Trust of my server's ECDSA certificate.