Configuration files are typically the settings files for things the end user can adjust. The "flash files" is essentially the operating system for the hardware, and with it defined parameters for what it communicates with and how. You have lots of control over the configuration files, you have no control over the flash file, it is all within the control of the manufacturer of the controller.
The ECU (or ECM depending on what the manufacturer wants to call it) is under the control of the engine builder. ECM files are tightly regulated and require validation by various organization for mostly air pollution compliance, but also things like safety and reliablity (like ABS, FM or DNV type certifications).
Engine ECU software also has two parts, a flash type file that sets the fixed programming of the ECU, and the configuration files for end user adjustable settings. There are usually two versions of the software (in CATERPILLAR's case there are three) one for end users or thrid party service vendors, and the dealer or authorized service provider version.
Power Wizard is a software package for the controller only, at least as far as I know. It allows you to install factory generated flash files when needed, but you can't make any changes to those files. It also allows you to modify customer parameters/settings and save a file for backup or reference. The software usually also has a functions to do better monitoring of parameters, such as see multiple parameters at once, and in some cases trend or log them.
The software for the Perkins engines is called EST (Electronic Service Tool), I'm sure of haw many versions of this software there is, I know for sure a customer version is available, but is limited to only changing customer parameters, in some cases I don't think it can download a flash file to the engine ECU. EST it actually the same software platform as CAT ET, your licensing determines how much capability you end up with.
The compatibility matrix(s) is a set of documentation that helps determine which versions of the controller firmware will work with what engine ECU flash files.
If you're looking for additional capability from your controllers with existing engines, you really do need to work with your servicing dealer.
The hardware platform for the Power Wizard does support Modbus RTU output, but I don't know if your flash file supports using that output and what parameters it makes available to the Modbus mapping, again you dealer is who you need to talk with on that.
Hope that helps, MikeL