Clearing the rear aperture on that set-up is very similar to doing the same thing on a Marlin SBL, or even on any rifle with an exposed hammer like many break-open single shots. I always find that raising the scope high enough to clear that rear aperture or hammer just makes it very uncomfortable to use without a raised cheekpiece, and it messes up the balance severely.
Maybe consider finding a scope with enough eye relief to mount low, right in front of the aperture. It allows a nice cheek weld and is better balanced; depends a lot on your physical build and shooting stance. I have gibbon arms and a long neck, and I find that a few scopes, usually lower-powered ones, can be mounted like that. It means that the aperture is visible in the bottom of the field of view, but I find it's easy to ignore after you get used to it.
Some so-called "scout" scopes can be mounted like that, and many scopes designated as "shotgun" scopes work as well. I have a couple of Leupold compact 2.5x scopes that aren't quite ideal but very close, and the Leupold variable scouts are very good also.
When shooting at game, the rear aperture is completely forgotten, much like the blast and recoil go completely unnoticed. In this pic, you can see how I could have used rings that were very slightly higher and would have allowed the scope to be moved back another 1/2 or 3/4 inch, but I prefer the low rings even though they forced the mounting position to be slightly further forward as shown. The eyepiece bell of the Leupold 2.5x is so close to the front beveled edge of the aperture base that a piece of paper just fits in between them. I also have a Leupold variable "scout" scope...1.5-4.5x, I think...that can be mounted in just the same spot. I can switch them back and forth using Weaver rings as shown (return to zero within about 1MOA) or proper QD's (even better return to zero) and find it's a very versatile set-up.
The front sight on the rail is good as a back-up, but the sight radius is pretty short and it's difficult to shoot the gun as well as you could with a longer radius, i.e. a sight at the muzzle. A red-dot on a QD mount can be sighted-in ahead of time, removed and carried in a pocket, and quickly mounted if needed in the field. You can even mount the red dot in non-QD rings on a 45-degree angled base at the front of the rail and leave it there all the time; just rotate the gun counter clockwise slightly (if you shoot right-handed) and it's right there...but it increases bulk and width of the whole package and I'm not in love with that plan.
