Yes, it makes a big difference.
Surfing is almost exclusively done with your hips, knees and ankles. Remove your ankles from that equation and you just made it (at least) 30% harder.
One of my best friends is a goofy surfer -- unfortunately, he's never owned or had access to a boat with a goofy wave. He's adapted and can surf as well as almost anyone on a regular wave while riding heel side. In fact, the one time we did get out on a goofy wave, he had no idea what he was doing.
I'd say he's the exception, though. You're going to have a tough time as a beginner learning how to surf that way. Regardless -- it took me about a year to "ride" the wave comfortably without the rope. Keep at it and you'll make progress eventually!
Former owner of a 1987 Supra Saltare. Current owner of a Malibu 23LSV.