In my experience, it's the only way to keep content of an unknown character set and highly diverse content from getting corrupted when going through processing stages (for email). A lot of the tools to manipulate an email message can (also) be destructive.
Email is weird.
I can see why they'd use it for this service, if the original email was also a part of the notification they're sending.
also first time i was sending sms messages and not using ascii trying to determinate the message length was fun. and by fun i mean gsm 7bit annoying.
Debugging something in an email message encoding in quoted-printable simply by viewing its source is doable sometimes. If it's in base64, not so much. I believe the size of your message would also be less using quoted-printable, rather than base64
Edit: a quick cursory google shows http://www.dpit.co.uk/decoding-quoted-printable-email-in-c/ as a good enough solution for C#. I feel kind of stupid now, but had honestly never heard of QP encoding before.