The answer is simple — It’s an incomplete view of the use of the WebPKI.
There are a number of different methodologies a web crawler-based approach might take in measuring the size of the WebPKI. The most naive approach would be to simply scan all IPv4 address space and log all of the certificates you see during this scan.
The problem is that this only shows a small fraction of the certificates that are out there. When you connect to an IP address and the associated web server doesn’t know what host you are trying to connect to it will return its “default” website and use the associated certificate.
That same IP address may literally be responsible for serving millions of sites based on the client’s indicated hostname. With this IP-based enumeration approach at best you would get one certificate from that host, at worse you wouldn’t even get that because some servers are not configured with a default site. This is just one problem with this approach there are many more.
Though most WebPKI market share reports do not document their methodology anecdotally it appears most work on this crawler approach and at least historically some have taken periodic drops from CAs to make their view “more complete”.