Is there any way that I can germinate seeds then transplant them to RootMaker containers as soon as they pop and still maintain RootMaker grower certification?

There is nothing wrong with germinating seeds in flats then transferring seedlings to RootMaker® trays – as long as it is done when the seedlings are quite small. This is what I practice at Lacebark for many of the species I work with – and primarily because seed germination can be so unpredictable and in order to get 32 of the same size in one tray, compared to a few big ones that over shadow the smaller ones.