Nothing wrong with your system. There is a huge amount of variation in how recordings are mixed and mastered. Multiple subs and room treatment will only help if you have low end booming issues. I have multiple subs in my system and constantly have to change the gain balance between the subs and the mains to compensate for the those differences.
The gain on some and maybe all of SVS subs can be controlled remotely with the SVS app from your phone. Another option would be to insert a DSP between your preamp and amp and then you could control the gain of either your sub or mains remotely with a laptop. Assuming you have a laptop, a miniDSP could be a good way to go. I believe they are rather economical and rather unobtrusive so your wife probably wouldn’t even know it was there.