Putting an Si5351 down does not make it inflexible, it can always be disabled (like that analog VFO). ?The SoftRock guys have an Si570 on some of their boards, but they took great pains to keep out any digital hash coming from the I2C host that drives it. ?Could be that a small processor on the radio board would be better than an arduino, as the board designer could include series resistors to keep edge rates down and choose crystal frequencies that won't interfere. ?And caps and ferrite beads and perhaps shielding. ?Hard to say what will make the most sense for a $59 transceiver.
Jerry, KE7ER