I wouldn't mind manually updating the cert and ket manually for one site...or even maybe five. But this process would get a little time intensive when managing 100s of sites.
Any ideas on next steps I could take?
Further explained by the support staff,
Namecheap is dedicated to data security and privacy for all internet users. We believe the movement to encrypt nearly all web traffic is a positive direction. As more sites embrace HTTPS and use of security products, providers of free SSL are beginning to come online. Though we believe increased web security is a good thing, we also think that using certificates from free providers can get more risk and uncertainty into your business.
The key distinction is that free SSL certificates provide encryption (i.e., scrambling of data during transmission to prevent tampering) only. Encryption is important, of course, but to get the crucial component of validation, you need a purchased SSL certificate. Validation refers to the security checks the Certificate Authority performs on your business before issuing a certificate. Validation assures users that certificate owners are who they say they are, building customers' trust in your business. Also, free SSL providers offer no integration assistance or other customer support.