although your question lacks a bit of relevant details for a decisive answer, in principle one can say, coverage reports are mergable, e.g. shown here

The two tools that are mentioned share similar output formats. Without having looked to deeply into the details, if there would be any overlapping format, i would configure those tools to produce reports in the same format, and find a way to merge them. An example for cobertura XML files is linked above. I expect this to work because i trust these reports to contain filenames and visited lines in a serialized format. Parsing these information looks like a manageble task to me.

Edit, because i forgot about the Azure part of the question: I'm not sure about the capabilities of Azure at this point, but i would not rely on it, if i can have a merge report from the start. It would be for a single code base anyway, as stated by OP.