I understand your concern but it will be fine. A lot of conversions are done this way--seems to work.
However, you may have some noise from the pump if you run the HP hose thru the stock lines or using a "quiet" flex line from one of the vendors. I have done two conversions using these methods and always had some noise until I went back to the stock Subaru HP hose from the pump that runs forward along L side of engine. There are some good posts on THE SAMBA about these issues and this stock Subaru hose conversion routing.
