Now JBDS Target Platform p2 repo uses default format to store packed with pack200 artifacts.

After digging repos available on eclipse I found a solution to control that. Magic is in format attribute of destination tag. Documentation says: "A URL to another repository from which to copy the repository name and other properties". It gave me an idea to find p2 repo on download.eclipse.org with jar.pack.gz files and check its properties in artifacts.xml. Soon I noticed a property that controls it

<property name="publishPackFilesAsSiblings" value="true"/>

So if you want to get rid of .blobstore in mirrored p2 repo just create artifacts.xml file like

<repository name="My repo with jar.pack.gz files" type="org.eclipse.equinox.p2.artifact.repository.simpleRepository" version="1.0.0">
<properties size="1">
<property name="publishPackFilesAsSiblings" value="true"/>
</properties>
</repository>

Then in destination tag format attribute use URL to folder that contains artifacts.xml file with content provided above and p2.mirror task will copy 'publishPackFilesAsSiblings' attribute to your local mirror. This will force mirroring task to store artifacts packed with pack200 as jar.pack.gz files.