You have a bundle with two packages: A and B
1) release version 1.0.0 of bundle
2) make a MINOR change in package A
3) remove package B
4) baseline the bundle against version 1.0.0
What would you expect the suggested version to be?
The actual suggested version today is 1.0.1
NOT 1.1.0, or even 2.0.0. Hence we lost a minor update on the bundle version.