This match between Afghanistan and Pakistan was major turning point for series. You pointed out that Afghanistan loss came down to bad stretch from 12th to 15th over when they only scored six runs and lost five wickets.
You also noted that Pakistan strong batting and excellent bowling were key to their win. Only Rashid Khan played little well but it was not enough to lead Afghanistan to victory. Given Pakistan strong performance I also think that Pakistan will win this Tri Nation series.
This is what will happen in the case of Afghanistan, either they will lose by a big margin or win by a big margin. The main reason for this is the nature of the XI. They have only 4 genuine batsmen, with which they will not be able to get good results every day. The day when their top order plays till the end and takes them close to victory, they will win only on that day. But the day when the top order gets out before getting close to victory, it will become difficult for them to build an innings. Because their XI has 4 batsmen, 4 all-rounders and 3 bowlers. It is normal that all-rounders do not play well regularly. So I think until the Afghanistan XI reduces the number of all-rounders, they will not do very well in international cricket. It may raise hopes, but it will not last in the end. On the other hand, Pakistan is still the best to win, their XI has 6 great batsmen, 2 all-rounders and 3 bowlers. That is why they are doing well in every department. Afghanistan played with half the team in the batting innings.