I know this is not your purview but was hoping someone here has dealt with this and can offer some insight.
How can I require client ssl cert authentication for a site but allow LE to bypass the client cert check for automatic cert renewal? i have not found a configuration that works.
The easiest solution would be to disable redirecting from http to https for .well-known/acme-challenge. Webroot authentication takes place over HTTP, not HTTPS, so if you can avoid redirecting, you avoid the client certificate issue altogether.
For example, the block you already have that does this redirection probably looks something like this: