For the Loba bundle, that is by design. That bundle is only meant to require that you do not own either the R-301 skin or the Loba skin. I am definitely not the "decider" of such things; only one of several people who can - from a technical capability standpoint - make certain changes / fix things / etc. I can/will make sure feedback is received by the team that does make these decisions.
In the case of the Octane bundle, we did not mean for owning Octane (the character) to prevent purchasing the bundle; in the case of the Loba bundle, the exclusivity was intentional. That was the point of my edit in my OP:
EDIT: there will still be some of these types of bundles where a "core" item may be something you already own and which will disqualify you from a bundle you'd like. We are watching that feedback and are trying our best to balance how we structure these things.