With the switch to SChannel with Connector/C 3.0 this seems to have stopped working.
Schannel converts PEM (base64) to DER (binary). It looks like it's not possible with the SChannel/Crypto API to read more than one base64 section.
This also affects all connectors building upon the C one, like our Connector/ODBC.
MySQL ODBC 8.0.13 on the other hand seems to support such PEM files just fine.