Unfortunately this is a very complicated question and there is no easy answer.
Are multi-carrier flights booked with .. services like Kiwi.com or GoToGate better for the environment than regular flights or worse?
There is no first order difference in how you book. Kiwi offers non-stop flights and mainline airlines offer some really convoluted itineraries as well. Ironically the more complicated itineraries are often cheaper since they are less convenient for the customers. Airlines price by supply and demand, not by actual cost.
What matters primarily for carbon emission for an itinerary are the number of legs and the distance flown, not who you book it with. In this regard shorter itineraries with less legs are better. On short hauls, takeoff itself can take up to 40% of the entire fuel consumption, so having a non-stop is often the most emission efficient option. Fuel efficiency depends on distance flown with "mid range" distances being the most efficient. For a Boeing 777-200 the optimum is around 4500km. In some cases it can be more efficient to break up a very long flight into two medium sized segments.
A secondary driver is the load factor of the plane. The incremental emissions from carrying one more passenger are actually quite small. A full plane is more efficient in terms of "carbon per passenger mile" simply because there are more passengers for almost the same fuel.
This being said, moving one passenger from flight A to flight B makes no overall difference. It just makes flight A less efficient and flight B more efficient. The total emissions stay the same (more or less).
The real win of load factors only comes into play when capacity and/or demand shifts enough so that entire flights are added or removed from the schedule. If and how this is impacted (or not) by booking through Kiwi vs. (say) United is anyone's guess, but I doubt that there is a significant correlation.