Makes sense - we aren’t trying to suggest you create a site per customer, although some other customers of ours do that as it better accommodates their use case.
You may be able to add up to 90 custom domains per site (that is the HARD limit which is not changeable) but I have to warn you this pattern will have some caveats which I discuss below. You can configure names via API to automate your usage, and you will have to “shard” your sites for names beyond the 90th.
The main caveats (besides needing to pay to resell our service) are really around SSL. We only serve SSL content, so any hostname we host must be covered by an SSL certificate. We can absolutely provision certificates for dozens of distinct names (and this is why we have a limit on # of sitenames since our SSL provider can only add a limited number to a certificate), but they ALL have to be configured right for this to work.
Using customer-provided domains where they control DNS will be a lot of troubleshooting overhead - for you, not us - since you’ll provide tech support to your customers on configuring DNS. We have a couple folks who use this pattern today, and I have helped them help many of their customers get things configured more correctly to allow SSL to provision. They have finally learned all the gotchas, but it was a lot of work for them and not a great customer experience for a lot of their customers. TL;DR it is hard to get right, and it will be a fair amount of work for you to provide tech support to them.