So, a workaround for this issue was found in mailing lists: http://dev.eclipse.org/mhonarc/lists/tycho-user/msg03277.html
To solve the issue one should add the following sections to POM and build.properties:
<build>
<plugins>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>target-platform-configuration</artifactId>
<version>${tycho-version}</version>
<configuration>
<dependency-resolution>
<extraRequirements>
<requirement>
<type>eclipse-plugin</type>
<id>org.eclipse.swt.win32.win32.x86_64</id>
<versionRange>[3.0.0,4.0.0)</versionRange>
</requirement>
</extraRequirements>
</dependency-resolution>
</configuration>
</plugin>
</plugins>
</build>
build.properties:
extra.. = platform:/fragment/org.eclipse.swt.win32.win32.x86_64
I have also updated the GitHub repository