Setting Calorie goals correctly

BMR is an irrelevance apart from being a start point to apply a multiplier get to an approximate TDEE.
It's your Total Daily Energy Expenditure that is your maintenance number. On here it's expressed as your daily goal + exercise calories when you set your goal to "maintain current weight".

The activity setting on here excludes exercise remember. Working a desk job (IT) does push you towards a sedentary setting but depends what else you do in your general day to day activities as well. It's just a start point so not worth too much agonising over TBH. You can manually change your goal based on actual results later on.

Disagree about not logging strength training - an hour would be about 200 - 250 cals (log under cardio section of your diary - search for strength training). If you are calorie counting it makes no sense not to log a significant amount of calories. You would log 250 cals of food wouldn't you? Doing that five days a week and not logging it would badly skew your numbers.

Will strength training increase maintenance levels? Yes, doing the exercise itself burns calories. That you may have a slightly better body composition as a result has a very minor effect on your calorie needs.

The initial weight loss isn't a great guide to your fat loss - reducing intake will result in less food in your system and a good chance of losing some water weight.
Would discard the first two weeks data and then monitor your weight for another couple of weeks to get a better idea by your rate of loss.

Food logging:
Don't go by scoops, cups or spoons. They measure volume not weight and the calories in food is in relation to weight.
That scoop of protein powder could well be very different to the 30g you expect for example.
You should see how much peanut butter I can get on a spoon!

It's not actually necessary to be ultra precise but you do need to be consistent. However, if your results over time don't seem to make sense then food logging inaccuracy is the prime suspect.

Oh, and I get the impression you'd appreciate the science and wit of this awesome guy:

http://physiqonomics.com/articles/

On the TDEE question, there are 2 ways of doing this. Either the TDEE - 20% or the way MFP is set up.

MFP works out your estimated NEAT, which excludes exercise specifically. It gives you a calorie number based on your NEAT and desired weight loss. You then add back calories burned exercising and eat those.

TDEE includes everything, and you work your deficit off this.

Now MFP works on 500 calories per day deficit to lose 1 lb per week. SO 1,000 cal deficit to lose 2 lbs.

Most TDEE calculators deduct a percentage off the end total. So while the two methods give the same calorie burn for a week, the deficits can be different (and weight loss can be different). Don't worry but it confused me at first.

So, the question is which do you use and does it matter. If you weekly activity is pretty consistent, then TDEE seems to work better. It gives you an average calorie limit per day regardless of whether it is a cardio or weights day and a lot of people like that consistency and not having to calculate the daily number. On the other end, some are not consistent (me, but I'm getting better) and so use the MFP and change up their calories every day based on what they did that day.

Both work and it does come down to personal preference and lifestyle. And, whichever you choose, MFP still works as a great tool for tracking calories. Just set your own goals and don't worry if some days are in the red and others are well under.

And if all this just confused you, then ignore it and keep doing what you are doing. Track your weight loss over time and shoot for 1% of your weight as a loss per week. Go by your results over a few weeks to decide if you calorie goal is correct.