I think there is a confusion between altimeter setting (ie QNH set on the altimeter) and altitude.
I have never seen X-plane change automatically the altimeter setting (in real life, altimeter setting can only be changed manually)
Let's say you are cruising over A at FL340, which is 34000 feet displayed on your altimeter with an altimeter setting of 1013 HPa (or 2992in.Hg). QNH over A is 1003 Hpa, So your real altitude is 34000 - (1013-1003)*28 = 33720 feet.
Now you reach B, your METAR (ie atmospheric properties) is updated abruptly and QNH is now 1023. In real life, the QNH change wouldn't be so abrupt and while still flying at FL340, your real altitude would now be 34000 -(1013-1023)*28 = 34280 feet.
But in the sim, you are still at a height of 33720 feet so your autopilot wants to reach that updated target height of 34280 feet in order to display 34000 on the altimeter again, which still has the setting of 1013 Hpa.
So in this theoretical case, before METAR update, your altimeter would display 34000. After METAR update, it would display 33440 and your autopilot would go up by 560 feet in order to reach the updated FL340.
It is more a problem of abrupt atmospheric property transition. Is that what you observe?
PS : I am not affiliated with Laminar Research.