So, I figured out a solution that allows me overlay the artifact without messing around with the source directory. Instead of slapping all of the files I want to overlay on top of the artifact files, I realized a simpler way would be to expand the artifact, remove the duplicate classes/resources, and use it as an additional source. I created my own plugin that takes as many 'source' directories as I want and it filters them in the order loaded.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>unpack</id>
<phase>initialize</phase>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>com.sample.service</groupId>
<artifactId>sampleService</artifactId>
<classifier>sources</classifier>
<type>jar</type>
<overWrite>true</overWrite>
<outputDirectory>${additional-source-folder}</outputDirectory>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>mn-stateadvantage</groupId>
<artifactId>duplicateSourceRemover-maven-plugin</artifactId>
<version>1.0-SNAPSHOT</version>
<executions>
<execution>
<goals>
<goal>removeDuplicates</goal>
</goals>
<phase>generate-sources</phase>
<configuration>
<sourceDirectories>
<param>src/main</param>
<param>${additional-source-folder}</param>
</sourceDirectories>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>add-source</id>
<phase>generate-resources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>${additional-source-folder}</source>
</sources>
</configuration>
</execution>
<execution>
<id>add-resource</id>
<phase>generate-resources</phase>
<goals>
<goal>add-resource</goal>
</goals>
<configuration>
<resources>
<resource>
<directory>${additional-source-folder}</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>