Is there any way to set ContextCapture to process orthoimagery at the lowest ground resolution available?

We have flown a dataset with multiple flight elevations. I am wanting to use the lower flight as my processing subset of data to essentially stich together to create my orthoimage. When flying at the lower altitude, we may not have captured features such as building/roof edges with enough of a nadir profile to touchup in the Reference Model. When we include the higher altitude photos to process with the lower altitude, there is a staunch contrast in ground resolution when stitching the photos together on the orthoimage. I am wondering if there is a way to process only the lower altitude photos but include the higher altitude photos to be available for touchups?

For reference - For data collection, we are using an RTK eBee X with an Aeria sensor flying at 200' ATO for a ground resolution of .5" for the lower altitude and 800' ATO for a ground resolution of 2".