It would be interesting to see if there’s something about those sites that nonetheless has a different configuration from others; @sulliops, if you have an example of an LE-certified site that doesn’t exhibit this behavior in Safari, we could try to look to see if there is something different somehow about the cert chain it sends (for example, maybe it has to do with the order of the certs in the chain, whether the site sends an unnecessary copy of the root certificate, whether the intermediate is omitted, or something else).
@mnordhoff’s observation is correct—the web client sites are not official and are not operated by LE.