Answering my own question:
The PSOC Programmer offers the CLI "Command Line Interface". A documentation can be found in PSOC Programmer:
help -->Documentation -->PSoC Programmer CLI User Guide
There I found the function "PSoC4_ProgramRowFromHex(IN rowID)".
I will try this and report the result soon.
Well, there are 2 findings with PSOC Programmer CLI:
1) The desired way fails when trying to merge 2 Hexfiles and use PSoC4_ProgramRowFromHex(IN rowID). The CLI seems to need a hexfile created by elftool with the elftool metadata. It works, if I take a hexfile created by a elftool, but it fails, if I merge the hexfile with another one with config data.
2) There's another CLI function called PSoC4_ProgramRow(). It works fine, the row data can easily overwirtten by a customer with configdata.
Well the first way, I think, would be more general for different controller-manufacterer. Just merge two hexfiles.
If there are any possibilities to merge a program-hexfile and a configdata-hexfile, with correct elftool-injections, please let me know.