There is a huge difference( my experience) . It typically reveals itself in the wash. Low quality flannel pills . I have given up on the low cost flannels at Jo 'Anns it pills bug time on the first wash and continues to pill. The flannel that is "premium " at Jo Anns I have had mixed results , some pilled , some did not... so Unless they let me wash it in the store to test ... I just pass .
As for quilt shop flannels I have had better results , but have had one or two pill slightly , but nothing compared to the pilling in the Jo'Anns flannel.
I have been a very reluctant buyer of flannel. At the quilt shop , I expressed my concerns , and the owner signed my receipt that she would refund my $$$ is I had pilling. Now that kind of commitment I will pay for.
I suggest you buy a bit from Jo'Anns and wash it and see if it suits your purposes, before buying any real yardage.