I am not sure I fully understand your question, but based on your questions I think you may not fully understand the situation, so I will provide a basic overview.
The PUC in the Beovision is loaded by the dealer with the required STB IR converter code, so the output of the PUC is controlling your 3rd party STB via an infrared transmitter physically stuck on the front of the 3rd party STB.
The B&O version 3.87 Beo5 Configuration Tool is used by the dealers and others who have received a copy to programme the Beo5. There are standard product configurations built into the tool for products such as the Beovision 10 and each Beovision often has different facilities and functions which need to be included.
When the Beo5 has been programmed to control a source device which is a 3rd party product controlled by the PUC, the Beo5 sends standard B&O infrared signals (not the 3rd party box signals) to the beovision and the Beovision converts these commands to the assocated 3rd party product which was selected for the associated I/O port via the IR transmitter.
So, you are asking me "Why does the Beo5 not control the 3rd party product without the use of the PUC ?" The answer is it can provided you produce an XML file for that product, BUT it is better to use the PUC for several reasons, one reason is you may not have a Beo5 and use a Beo4 or have both remotes which means you can still control everything. Another reason is if you control a STB directly from the Beo5 it needs to be visible to the Beo5 infrared signal, but most people want to hide the STB's away out of sight.
You also asked about "Exporting Configuration" are you talking about saving a template or the whole configuration (configuration.xml) ?