RE: Is it possible to only sell a product in a bundle?
Hi,
Quote has no direct relationship with Product.
So what you need to do is to restrict creating the quote line record whose product (lookup field) is not bundled.
When a product is bundled, there will be a Product Association record. (Product Association: Product = N: 1)

If you are using Dynamics Sales only, the kit will not be involved.
So it means that if there is no related Product Association record, the product is not bundled.
A real-time workflow targeting at Quote Line entity can be created.
If the Product has 0 child Product Association record, cancel the creation of the Quote Line.
As there is no OOTB step in workflow to count the child records, you can download the following solution and import it into your environment.
Dynamics-365-Workflow-Tools
It includes a method to achieve the counting.
Dynamics-365-Workflow-Tools/CountChildEntityRecord.md at master · demianrasko/Dynamics-365-Workflow-Tools · GitHub