Check my understanding

If you have correctly identified your activity level and log everything that passes your lips then YES you will lose weight. MFP does have a tendency to 'over estimate' calories burned on exercise, so you could just eat 50 to 75% of them back and still be OK.

I, like many others have been using the Road Map instead of MFP calculators. A fellow MFP'er Helloitsdan, put together information and calculators which give you a more personal assessment of your calorie goal. Another MFP'er Heybales also created a spreadsheet where you just pump your stats in and it does the work for you based on the same calculators. The spreadsheet in particular gives you a clearer definition of your activity level and with this method you tend to use a final calorie goal that includes your activity & exercise which will be higher than MFP, but you do not eat back your exercise calories.

The links are:
http://www.myfitnesspal.com/topics/show/654536-in-place-of-a-road-map-2-0-revised-7-2-12 <

https://docs.google.com/spreadsheet/ccc?key=0Amt7QBR9-c6MdGVTbGswLUUzUHNVVUlNSW9wZWloeUE

You are correct. The reason is that MFP calculates your optimal calorie level for weight loss (your deficit) with no exercise factored in. So if you exercise and burn more, in order to keep the same deficit, you need to eat more. The problems come with overestimating calories burned, and mis-estimating your overall calorie requirement and intake. Also, people attempt to lose weight too fast, which gives them too big a deficit and makes it harder to lose. Since everything is really just an estimate, it's best to be flexible -- try something for awhile, see how it goes, and tweak as needed. The MFP method and road map method will both work if you use them this way -- the road map method just gives you a slightly smaller deficit.