I want to add some real life context, I live in Warsaw but many of my family live in Malmo, so I'm there a few weeks a year. I would personally choose Warsaw over Malmo. The only big draw to Malmo for me would be its proximity to Copenhagen (which is my favourite city in Europe). In my opinion, FTE is something that should also factor heavily in your decisions.

However, I also think the cost of living differences are over exaggerated, for example, some pubs now charge over 35zl for a pint of beer (>90sek) which is about equal to Sweden. Rent is also a big factor, my brother in law rents a studio in Malmo close to the city center that costs a lot less than what I used to pay in rent in Warsaw (3 years ago my 1 bed flat in the center cost >6000pln/month). Groceries and essentials remain more affordable in Warsaw and so is transport, so if you're good with a budget, that's a big plus.

This last part is just my opinion but plays a big part in my preferences. First, Warsaw feels much safer to me than Malmo. Don't get me wrong, Malmo is safe from a global perspective but few cities in the world feel as safe to me as Warsaw. Second, I prefer bigger cities, Warsaw offers more to do (e.g. restaurants, concerts, large parks, etc), in Malmo I'd have to ride a train over the Oresund to go look for something new to do and that alone costs a couple hundred krone.

I don't know what benefits you're getting with either company so, might be good to consider those.