If you think logically for a sec, you want to lock your receiving device to Fref. You do not want it to lock to 2Fref, 3Fref, etc. Therefore having a clean sine wave Fref makes sense.
It depends what you want to use the reference for.
If all you're interested in is frequency, many pieces of equipment used some variation of a comparator to square up the reference so only the zero crossings were significant and a 'distorted' sine wave or square wave might be desirable. But if you wanted to multiply the reference, then you might want a clean sine wave.
A common architecture has the internal reference phase-lock to the external signal. That gives you a known quality reference - the internal one - that matches the frequency of the external reference.
Some equipment will lock to harmonics or subharmonics, some ignore them, some have that as an option. Input impedance for the Ref-In jack varies from 50 ohms to hundreds of Kohms. Amplitudes are similarly variable. I typically run a daisy-chain from unit to unit and then terminate the chain with a 50 ohm terminator. (Anyone remember 10Base2 ethernet?)

Ed