Can you tell me a bit more as to why you are looking to hide the colour variant at checkout as well as the product and cart page? Does the customer not have a choice in which colour they are purchasing? If so, why do you keep the variant on the product itself?
The simplest route to take would be to delete the variant itself. Edits to the checkout layout and design outside the theme editor are strongly discouraged and not supported by Shopify. To hide a specific product variant on the checkout page would require some intensive code changes that will likely affect the procedures in place to ensure a secure checkout for your clients.
I look forward to your reply with a bit more context here.
Your client could consider having a stand-alone product made for the separates that include the three variants but the product itself can remain hidden on the website. You would essentially keep the Product status as “Draft”. That way, there’s no way a customer may stumble upon it online and the inventory will be tracked through the platform in the backend.
Alternatively, with the Shopify Plus plan, customizations to the checkout that are in line with increasing the functionality of the business can be considered. The Plus plan allows for such customizations on a case by case basis since your account manager would oversee this directly and ensure that the safety of the checkout is not compromised. With that being said, this is not something I can confirm for certain - only a Plus member would be able to discuss this further with you.
If you believe that the Plus plan is a possibility for your client, you can reach out to the team directly here: https://www.shopify.com/plus.
I hope this helps. If you have any other questions, please let me know.
It’s been almost a year since this post, no response? The variant.title is by default displayed under the product in the new checkout extensibility upgrade with no option to hide it?