Outside of the Azure Devops world, the situation you describe seems trivial to me.
Simply make sure to configure JaCoCo goals prepare-agent and report. For example on my test project, I simply added this code:
<profile>
<id>coverage</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.5</version>
<executions>
<execution>
<id>prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
to the root pom and… that it. The coverage is correctly imported.
Every module will generate his own report, and it will be used for analysis, finding the report in the default directory.
By the way, this nice guide exists for basic JaCoCo setup, with project examples. In your case, you don’t even need to look at the multi-module part since you are not interested by cross-module coverage.
At this point, could you try to analyze your project with a local instance of Sonarqube? It would enable you to have more control over the analysis and identify more precisely where the issue comes from.