The Si5351 does generate square waves. As the frequency goes up, the square wave tends to round off, that or my scope (100MHz) may be filtering the signal at the 70MHz and 45MHz areas of the transceiver. Regardless, I too have corrupted sine waves on the other two clocks, the high one almost a sine wave. This could also be related to how long the signal runs are from the Si5351 to the mixers.
Good luck with the new antenna. That is the most important area for good operation.