Hi,
The verification email is not sent by the Joomla JUser save. It's specific code in the controller which does that.
I know since we have the same capability in HikaShop and we actually send our own verification email if the setting is activated in Joomla while still using the Joomla user API to add the user to the database.
So the fact that the verification email is sent doesn't mean that the user is added using the Joomla user API. That's unrelated.
Looking at the "save user" action of Chronoforms is indeed what I woul recommend, or ask the developer directly.
But yes, updating the user_cms_id yourself it totally fine. You might even prefer doing it like that as if you trigger the onUserAfterSave event, you might have issues with other plugins.
For example, captcha plugins also implement that event and thus the captcha plugins aren't properly called to display on the registration form, they will cancel the registration if you go through Joomla user API for the saving.