You don't need a workaround. You create a BA that chooses that same
versions should upgrade. The wixstdba does not choose to do that today.

To be clear, the old bundle is not "overwritten". The new bundle comes
along, finds the old bundle there and (by default) tells the old bundle to
remove itself (at the end of the chain, after whatever is in the new bundle
is removed).
Package reference counting in Burn handles your second scenario seamlessly.
If you want the new bundle to replace the old bundle, and you want to use
wixstdba, then the new bundle has to have a new version. When you do that
then the new bundle will run, detect all the packages, find that only one
needs to be major upgraded, do that, then launch the uninstall of the old
Bundle will will uncache the old upgraded MSI and clean up its registration.
Look at the log files and you can see this all happen.
On Wed, Sep 26, 2012 at 11:45 PM, Neil Sleightholm <n...@x2systems.com>wrote:

> Ah the same version upgrade problem - I have questioned this quite a bit
> on this list and raised a defect http://sourceforge.net/p/wix/bugs/3065/.
> There isn't a workaround in WiX other than changing the bundle version
> (yet) but if you have your own BA I have put some code in the defect that
> should allow this to work.
>
> Neil
>
>
> >Experimenting a bit.
> >
> >Installing a newer version bundle over an older one causes the old bundle
> >entry in Add/Remove Programs to be overwritten with the new one, such as
> >going from bundle version 1.0.0.0 to 1.1.0.0. In the end I only get one
> >entry. The MSI that's packaged gets a major upgrade. (I assume changing
> >the
> >bundle's version means replace every package in the chain?)
> >
> >If I set up a major upgrade at the MSI level--changing the Product's Id
> >and
> >Version, but do not change the bundle's version, the MSI's files get
> >replaced with the newer ones. I get two entries in Add/Remove Programs for
> >the bundle. Both at version 1.0.0.0. Both have to be uninstalled before
> >the
> >MSI's files are removed. (I take this to mean a major upgrade of the
> >bundle
> >did not kick in because one version was not higher than the other. So WiX
> >has no choice but to leave both bundles installed?)
> >
> >I'm wondering, if I wanted to have one entry in Add/Remove Programs, but
> >do
> >a major upgrade to only one MSI package in a chain that had, say, five
> >MSI's. Is that possible? Will Burn upgrade just the one MSI, but not
> >create
> >a second entry in Add/Remove Programs? Or do you have to change the bundle
> >version, which I'm guessing would uninstall and reinstall all packages in
> >the chain? (I could be wrong about that)
> >
> >
> >
> >
> >
> >--
> >View this message in context:
> >
> http://windows-installer-xml-wix-toolset.687559.n2.nabble.com/The-bundle-s
> >-version-tp7580785p7580878.html
> >Sent from the wix-users mailing list archive at Nabble.com.
> >
> >--------------------------------------------------------------------------
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