I got an answer from the Fairphone support - and it seems eco charging mode still exists:
About the eco charging mode, it is an FP3 feature. It is designed to handle the phone charging more efficiently and assures the quality of the battery. To reduce the impact batteries have on the environment, the Eco charging feature on Fairphone 3 offers customers an efficient use of energy and a longer battery lifetime, and it’s enabled on the phone by default.
Also, about an app, we don’t recommend to use apps to improve battery life because they can interfere with the normal functionality of the phone.
Good to hear.