For example this connector that I'm planning to use Molex 2169890001 has D+ pins A6 and B6 which are on opposite sides and D- pins A7 & B7 which are also on opposite sides
Well yeah, you’ll find that basically all USB-C connectors’ pinouts are like that, because the USB-C connector has rotational symmetry — that’s why you can insert the cable either way. It’s impractical to make the PCB pins come out in an order other than the order of the contacts inside the connector, so the PCB pins will also exhibit the rotational symmetry.
but also separated by one pin and you couldn't even route trace between them.
Have you reduced your clearances to the minimum the PCB manufacturer allows? You might be able to route between them then. You can do one trace on one layer and the other trace on another layer.
SMD versions anre easier to lay out, since you can run traces below the pads.
See the attached photo, copied from
https://www.3dphotonix.com/post/usbcmuxAlas, the connector style you chose (the upright right-angle or “vertical flag” type) is one of the more exotic styles, with very few options. But I did find a few that are SMD:
LUB-C128D-007-G-19
USB4205-GF-A
USB4210-GF-A
Any of those would be easier to route.
Have you checked out how other products (especially open-source ones where you can download and inspect the PCB layout files) handle this?
FWIW, for USB 3 and higher speeds, you don’t even bother to try; instead, you use a multiplexer (MUX) chip and route each side separately. (You can see this in the image, and that topic is what the page I copied it from is about.)