SP includes those background calories and they're not normally deducted.
If you know that value by all means go ahead and subtract it manually, but no there's no box for that here. Most people enter the full value the HRM gives.
Yes, that's double-counting. That's one of the reasons it's always best to understate exercise if in doubt, rather than overstating it! :)
Basically, enter the full value, and see for 6-8 weeks if your weight loss aligns with the expected losses given the deficit you're creating. If not, maybe it could be that, and you might want to think about adjusting goals accordingly.
It shouldn't be a problem unless you're doing hours and hours of exercise daily. As you point out, the difference was normally 40 cals per hour. If you do an hour a day that's a whole whopping 40 calories difference - WELL within the margin of error considering everything you're entering (in and out) is an estimation anyway.
It's one of those things where yes technically it could be more accurate to do that, but it probably doesn't make enough difference to even bother about.