The target platform will contain both content from Indigo and Helios. Quoting the Target Platform wiki page:
In case multiple target platform configuration approaches are combined, the target platform contains the union of the content defined through each approach.
So for the dependency resolution, Tycho could either use Indigo bundles, or Helios bundles, or a mixture of these.
The resolution is based on the p2 planner which finds a valid solution to satisfy the requirements. In case there are multiple solutions, the p2 planner has a preference towards later bundle versions and a small set of transitive dependencies. These preferences often contradict each other, e.g. when a later version of a bundle has a larger set of transitive dependencies. So in general it is hard to predict which versions are picked in such a case.
So, if you need to know what your bundles are compiled against, use a target platform which appropriately restricts the available versions.