There's 2 variant related options in the Kaching Quantity bundle app. Lets take a look at both of them.

"Let customers choose different variants for each item" will enable variants selection for all bundle deals except single quantity deal

"Show product variants selection" in the single quantity deal will enable variants for the single quantity deal.

We did that by design to allow more advanced variants display combinations. For example you can disable variants for the single quantity deal and keep your main ( native ) store variant picker above bundle widget.

This is powerful because you can re-use more advanced variant picker selection above bundles ( e.g. swatches )