I am inclined to think that the existing set up will be alright but it could be improved.
One suggestion is to extend the exhaust by adding a piece of pipe to the coupling. Your measurement should be from the end of one pipe to the end of the other pipe rather than from side to side. Verify that the intake is the pipe with the 90*.
Your concern about gases entering the house is unfounded. Neither of those pipes connect to the duct system. However, problems can arise if the intake pipe is above the exhaust pipe which can draw the exhaust fumes back in to the combustion chamber. The decreased oxygen content will cause incomplete combustion and sooting.
Lennox originally specified 36" separation for the pipes for the Pulse furnace but even that distance was not adequate under all conditions. They then used the configuration shown in your photo. By extending the exhaust 10-12" from the wall the gases could disperse without being drawn in the other pipe.
If the pipes are close to the height of expected snow accumulation then they should both be raised with goose necks.
BTW, you may paint the outside of the pipes to match your siding.
Conclusion: As long as the vent gases don't recirculate, don't obsess over it.