Hi,
sorry, I've overseen that you use assembly variant without MGTs on PL side.
When you use TEBF0808 carrier, the SI5338 (this one on the TE0803 module, schematic page 25 component U5), can only used with the onboard 25MHz oscillator which is connected IN3 of the PLL. So you can generate different CLKs, like we do it in our reference designs
The same happens with the SI5338 on the TEBF0808 carrier, when you use TE0803 module.
TEBF0808 was original design for TE0808 which has bigger SoC with more IOs. TE0803 is smaller version, so not all periphery is connected on this combination of carrier and module.
So at the end you can't use external reference CLK for SI5338 on the TE0803/TEBF0808 combination. This is only possible when you create an custom carrier.
br
John