Tracking some of the trends on these for the last few years I am actually inclined to think that they might indeed be different alleles from one another. Not radically different mind, something along the lines of Baker-line Special versus TCR-line Special kind of different.
Now, as far as mixing the lines... Personally, I would be leery of blending them, for pretty much the reasons Ax outlined. But that is just me. Ultimately it is up to you on whether you want to move your project on faster or whether you want to keep pure lines.