Hello
When we tested the reported issue in our side, the partial payment functionality is working perfectly fine with both the standard PayPal and PayPal express checkout.
Please verify the issue in your side by enabling use global payment percentage option by going to Admin Panel > Trips > Individual Trip > Dates and Prices > Minimum Payout option
Screenshot : https://prnt.sc/p0jo3i
On Disabling this option, the partial payment percentage is set from the individual trip which is by default 10%. When you enable the global option, the partial payment % is set from the % set in Admin Panel > WP Travel > Settings > Payment > Partial Payment
Screenshot : https://prnt.sc/p0jp9h
Hope this helps.
If the issue still persist in your side, feel free to write back to us.
Best Regards!