I'm considering applying for the AF HPSP scholarship and have extensively looked up a lot of information. This is what I have found in regards to your questions. Hopefully someone who has gone through the whole process can add or clarify my answers.
#1: After dental school you become active duty and work full time as a dentist in the military. You are also on the third tier of the officer hierarchy, as a Captain, which is pretty impressive. Your compensation becomes much better than the living stipend you received while in dental school. Instead of ~2,100 each month (~25k/year) you would now earn roughly 91K/year. You receive your captain pay + housing stipend + sustenance stipend + dental profession stipend which totals to 91K/year. This is the income you earn even if you are in residency program while in the military and not just a general dentist. What is good about this system is that you're effectively being taxed at 60-70K/year which makes that 91K stretch a litter further than it would in a civilian setting. Also, you will have access to tax free groceries and goods if you decide to do your shopping on the military base.
Tax free groceries it may be, but not surcharge free.
You bring up a question I have also been interested about, from what I have read it appears that your income will actually take a small jump up from 91K during or after your residency program but I haven't found enough posts to thoroughly substantiate that. I read about an AF OMFS resident mentioning that after his 2nd year of residency he was making a little more than 100K a year... so I assume they recognize your additional skill set and compensate you accordingly. Anyone else have specifics on this?
Your base pay goes up based on your rank and years in service. Housing allowance changes from location to location, year to year. You can qualify to a retention bonus once your initial obligation is served.
#2: That's right, after residency you would owe them only 3 years doing endo. You are paying off the residency years concurrently as you're in the program, thus making them neutral. Someone actually described it as, you are still paying off your dental school years while you are in the military residency program thus after your 2 year residency program you still owe them 1 year for the HPSP and 2 years for the endo residency... It's easier just to consider the residency as neutral years...
That's assuming you get into your endo residency right away. If you already served out your HPSP obligation then get into a residency, then you will be serving them consecutively.
For both of your questions, the better scenario is what ultimately happens.