I would ask Hans to confirm,
he may have qualitative results. RF 101 says the 50W PA would amplify everything coming from the QCX+ of course, and without a pre LPF that will include all the unwanted harmonics. Relying on the final LPF to get rid of these at 50w may not be a good idea IMHO. The fidelity of that LPF would need to be very high.
As the PA is being used, I don't see any air miles in omitting the internal LPF as the gain would be negligible. Also the impedance matching of the PA to AMP may not be as expected.
The Class E amplifier is intrinsically linked to the highly balanced LPF.
My suggestion is to 1) Ask Hans, 2) don't omit it for the fear of unwanted issues in the Class E final amplifier stage. These class E amps are very susceptible all kinds of issues if the load/LPF is not correct.