You will be fine as long as intake and exhaust are not undersized for their individual run lengths. I'm starting to prefer this configuration actually, less need to capture condensate/rain on the intake and on the side you can clean out any debris that gets sucked in more easily. (spring when the air is full of seeds for example).
You can call their tech support to confirm calculations if you are unsure.
Only thing is they really do not test for this configuration so may not be supported (supported means they cannot help you troubleshoot and may require standardized venting if you had problems that pointed to pressure differential, doesn't mean it wouldn't work). There is a rare condition where there could be a localized pressure differential between the intake and exhaust positions that might cause the internal air pressure sensor to go into an error. I wouldn't worry about that though as it is so rare as to be inconsequential in practice unless the distance between vents is extreme or there is some kind of wind tunnel effect between houses causing low pressure at the intake. If it did happen you just reboot the heater.
