I think your stereo shop is misinformed... there's no way the speakers are connected to the deck via fibre. If that was the case, then each speaker would need its own power source, amp, and DAC to process the signal. I don't even think they make speakers like that. In addition, they go on to say that changing the speakers would change the system impedance. Fibre optics don't produce an impedance... but a traditional speaker does (e.g. 4ohm, 6 ohm or 8ohm speakers). Something's wrong with what they have said.
What I expect is that 3rd party wiring harnesses might not be available yet to connect 3rd party equipment to the deck, or they just don't know how to disassemble the dash. But the speaker upgrades should be a piece of cake as long as you buy the same impedance as the factory units.