Comparing the CR1a bits:

http://www.qa.jboss.com/binaries/RHDS/updates/development/5.0.0.CR1a.core.pde/ (built with .product job)
vs.
http://www.qa.jboss.com/binaries/RHDS/updates/development/5.0.0.CR1a.core.tycho/ (build with .updatesite job)

GOOD differences:

1. Tycho build is missing pack.gz duplicates of plugins
2. Tycho build lacks Eclipse UI/SWT plugins related to unsupported platforms (OSX Carbon, Solaris, etc.)
3. Tycho build only includes a single version of a plugin; PDE build includes multiples of plugins such as apache.commons.logging
4. Tycho build is missing javax.el, com.springsource.javax.servlet.jsp, com.springsource.javax.servlet, com.springsource.javax.el plugins
5. Tycho build is missing images/ and web/ folders (which are irrelevant in an update site and only applies to the web UI for the update site)
6. Tycho build renames "com.jboss.jbds.all_root.<ws>.<os>.<arch>_5.0.0.TIMESTAMP" binaries to "com.jboss.jbds.all.executable.<ws>.<os>.<arch>_5.0.0.TIMESTAMP-Hxx-SUFFIX"

Questionable differences:

1. Tycho build is missing org.jdom.jaxen plugin
2. Tycho build adds org.jboss.tools.xulrunner plugin, org.mozilla.xulrunner.feature, org.jboss.tools.xulrunner.feature
3. Tycho build adds org.eclipse.net4j.jms.api plugin
4. Tycho build adds org.eclipse.equinox.executable plugin
5. Tycho build adds org.jboss.tools.usage.feature
6. Tycho build adds com.jboss.jbds.central.discovery.feature and com.jboss.jbds.central.discovery plugin