Right, so my question is how could a, at the time, geographically small entity such as Rome in 281 BC could field an army of 40,000 against Pyrrhus despite the fact that at the time they only controlled central Italy. Meanwhile, the Holy Roman Empire during the dark ages could only field a couple thousand at most despite "controlling" most of Europe. This screams logistical changes, and I may be wrong, but in the case it was a logistical change, what was it? Also how did logistics fall so far that knowledge of amassing armies from a thousand years earlier was somehow more advanced?
You are correct that it is a matter of logistics.
You are not correct in assuming the knowledge has been lost.
The concept of feeding a huge army with grain delivered from sources all over the nation is not exactly lost, but rather difficult to put into practice.
Logistics isn't simply a matter of 'I have declared that we shall feed the army using a supply train, here are the numbers'. Material realities had to be considered as well.
The most glaring issue in the 'dark ages' is that land-based transportation had essentially broken down. Roads were in disrepair, and the countryside was full of brigands. (Daily Life in the Age of Charlemagne By John J. Butt). As such, the delivery of food over a huge distance to a huge army would necessitate correspondingly large numbers of troops deployed simply to guard the food being delivered.
To put it simply, the logistical breakdown is a symptom of general economic recession, rendering previously workable systems too dangerous to put into practice.