Why does one often have to check in extra early, i.e. 3-4 hours early, before the flight departure for (covid-19) repatriation flights?

The additional check in time is needed for all the extra paperwork. Repatriation flights are organized and approved by governments to help return citizens to their country of origin. They can't let anyone on board who is simply willing to pay the fare. They must check and double check your passport, citizenship status, etc. Moreover, scheduling a repatriation flight is not the same as regular commercial flight operation. The planes often arrive empty, without a regular gate to occupy, without a regular slot to fly and the whole operation can be changed at the last-minute. If you really want to get on the flight then it's best to be there extra early to deal with the unexpected.

In addition to jcklopp's excellent answer, the other reason they want you there early is that they absolutely do not want you to miss this flight. Repatriation flights are "last chance" flights, and there are two nightmare scenarios that they want to avoid at all costs. One is where they have to delay the flight to wait for someone who hasn't arrived, possibly requiring new permissions from the departure country and possibly endangering the people who actually made it on time. They so dislike this that they probably won't do it, leading to nightmare scenario 2 where someone who should have been evacuated is left behind in a dangerous place. Almost by definition repatriation flights are coming from places where travelling to an airport is going to be more difficult than usual, so aiming to arrive very early gives and extra buffer against being late.

As an employee in an airline that is currently operating many repatriation flights, I can confirm both answers from @jcklopp and @DJClayworth and add one more reason, that is the health briefing.

Repatriation flights related to the COVID-19 situation have very special health precautions and passengers must be briefed in advance before boarding. This includes masks and gloves distribution, seating policy (one seat must be empty between passengers, etc.) and lavatory usage, food distribution and collection. Also, identifying potentially infected passengers.

Most of these temporary precautions must be adhered to once onboard, otherwise, there is no use of them, so passengers will be briefed by the ground staff in advance, which makes the boarding takes a little extra time than usual.