Well, if the conduit can't be recessed, then the only resort is to uninstall it, then install the siding, then reinstall the conduit on the OUTSIDE of the siding. If you had, for example, gypsum board for sheathing, you could conceivably cut out the gypsum so the conduit could be recessed.
Oh, there is one last option. If possible, re-route the wiring so the 'end point' of the line is where the box is. If you have to run a separate circuit from the basement or something, that's what I'd do. It shouldn't be that hard since you already have the old siding removed. There are vinyl fixtures for things like electrical outlets, hose bibs, and light mounting blocks. There are even vent fixtures. All this can be had either at places like Home Depot or by ordering from them or off the WEB. (BUilder's Edge makes a lot of these accessories.)
Anyways, now that the old siding is off, now is the time to add new/additional outdoor faucets, lights, and outlets. (Be sure that whatever you install is rated for outdoors, ie., GFCI outlets w/covers.) If you need more, post up! My best to ya and hope this helps.
Jay J -Moderator
PS: Hopefully, if you re-route your wiring, you have a 'block' on the breaker box. If not, you'll have to evaluate everything that's on your existing breakers to see where you can 'tap' into a line ...