Why do some airports shuffle connecting passengers through security again

Everyone else addressed the security concerns, so I’ll address another part of your post.

It’s bad from a Covid mitigation perspective: being jammed in a line for a long time is probably the single riskiest activity of travelling. Social distancing in security lines is NOT practical.

The exact same question was often asked in the context of terrorism: isn’t it bad for thousands of people to be jammed in security lines, creating a perfect opportunity for an evil person? The answer is… sure, it’s a risk, but no one believes in that risk seriously enough to do something about it. So with the exception of Israel, every other country lets giant dense lines form in unsecured areas of their airports.

The same applies to COVID as of December 2022: with the sole exception of China pretty much every other country has decided that the risk of the virus spreading is too insignificant to actually do something about it, so no one cares if a few thousand extra cases show up every year because these security checks. This might the right or the wrong decision but at the end of the day that’s the equilibrium and there’s not much anyone can do about it.

Your description of when additional security is performed is missing one important fact. To use your example airport of FRA, you’ve stated that there is no need to re-clear security when connecting from another flight. This is NOT always correct.

Many airports, including Frankfurt (FRA), will determine whether a passenger needs to re-clear security based on the origin of the flight they are arriving on. As you’ve stated in your question, when arriving from the US into Frankfurt there is generally no need to re-clear security. The same is also generally true for flights from other EU countries. (I say ‘generally’ because airport officials always have the ability to force an extra security check for passengers from these flights if they feel there is a need).

However many flights from other countries DO require clearing security on arrival in Frankfurt – in fact it’s a legal requirement that they do so under EU legislation. Any passenger arriving from an airport/country that hasn’t agreed to enforce the EU’s security standards is required to pass through security before being allowed into the departures area of the airport.

Rather than having to maintain separate arrival areas/gates/corridors for flights based on the origin of the flight, some other countries/airports take the more simple approach of forcing all connecting passengers through security before they are able to enter the departures area. London Heathrow as you’ve mentioned takes this approach.

There is an additional model which is worth mentioning, which is what used in the US. All passengers arriving into the US on international flights (with the exception of flights from a small number of "pre-clearance" airports where immigration/customs formalities are carried out at the point of departure) are required to pass through immigration and customs on arrival in the US. Passing through customs means that passengers have had access to their checked luggage, which in itself necessitates them re-clearing security as otherwise they could have removed items from their check luggage and carry them onto the plane.

You mentioned having to pass through security in IST (Istanbul, Turkey). Istanbul actually uses the same model as Frankfurt, in that it depends on the airport your flight is arriving from. For some flights, presuming you already have a boarding pass for your connecting flight, you will be allowed directly enter the departure airport without re-clearing security. For other flights, all connecting passengers will need to re-clear security.

Domestic transfers (in any country) would generally not require passing through security as the security rules at the origin airport would be the same as at the destination airport, given that they are both in the same country. However even then there are exceptions. For example, Australian security rules are different for flights on very small planes (eg, sub-30 seaters) that generally only fly from remote airports that do not have the resources to enforce security as would otherwise be required. When one of these flights arrives into a major airport (eg, Sydney) the passengers are forced to re-clear security due to them not having passed through proper security at their origin airport.