I run into the same problem and figured out that subversion looks for
valid "default" root CA certs within /etc/ssl/certs/ca-certificates.crt
if you set "ssl-trust-default-ca = yes".

To trust your own CA (and add it to the ca-certificates.crt),  proceed
with the following steps:

mkdir /usr/share/ca-certificates/example.com
cp Example_CA.crt /usr/share/ca-certificates/example.com/.
 
echo "example.com/Example_CA.crt" >> /etc/ca-certificates.conf
 
update-ca-certificates -v


Afterwards subversion accepts the server certificate.

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https://bugs.launchpad.net/bugs/474633

Title:
  svn client ignores the setting ssl-trust-default-ca

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