How to configure a MikroTik hAP ac lite router as a Layer 2 switch?

Just bridge every interface on hAP and it will act essentially as a switch.
That's it pretty much.

Then remove or disable any dhcp-server instances on IP > DHCP-Server.

Since you do not provide any configuration exports it's impossible to provide you with any commands on how to do the above since every mikrotik installation is kind of unique. You could have implemented your current setup in many different ways. We need to know your current configuration to be able to provide you with any commands.

DHCP relay has nothing to do with what you ask so don't confuse yourself with that.

Also, winbox works fine on Linux using Wine. That's the official way of running Winbox on non-windows machines.

Without winbox it just makes the whole procedure that much more difficult since you might lose access to mikrotik in order to change its IP to the FritzBox subnet (Winbox can find and connect to a mikrotik router even if it's not accessible via IP). If you don't understand what you are doing (blindly copying/pasting commands) you may end up having to reset the whole configuration to gain access again.

IMHO you should configure the FritzBox to act as a PPPoE bridge and use Mikrotik to dial (pppoe-client) to the ISP to establish the internet connection.

This way FritzBox will act as a modem and nothing more. And hAP will act as a powerful router. Having Mikrotik obtain the public IP you avoid double NATs and most importantly you can take advantage of all mikrotik's features. You can create very advanced configurations that I highly doubt that FritzBox (or any other consumer dsl modem for that matter) can do.