My SMS-1's volume setting isn't that high, but you're going to see a fair bit of variation and I wouldn't worry about it (for that matter, I felt funny setting my SMS-1's volume as low as I did, would have felt less odd about setting it up around where you have it).

If you have a dip or other activity around 125Hz, it's nothing that the SMS-1 can help with. Not only is your crossover probably set higher than that (meaning that the sub is no longer active at that point, at least with the SMS-1's test tone), but the highest position that you can set an EQ to on the SMS-1 is 120Hz even if you did raise your crossover that much - not something that I'd recommend doing. Also, I think that the SMS-1 is not intended to continue to provide accurate results all the way up to the end of the scale since it can't apply EQ all the way there. In my experience, it seems to start to roll off around 160Hz or so. Once you get too much past 150Hz I don't know how precise the display is.