Religious architecture has historically been a catalyst for the creation of communities, places and new and innovative construction. It encompasses a huge array of architectural styles and themes because, unlike most other architecture, is fed from the beliefs, motives and religious faiths of those that worhip within them. Each place of worship will as such vary according to the particular practices and nuances of the religion in question, and we can even see that different branches of the same religion will also show variation.
It would to too exhaustive to go through a complete set of examples, but many of us will be familiar with the concept of a "traditional" christian church or cathedral. And this is as good an example as any of how beliefs and symbols are used. For instance, the structure was historically aligned in order that the congregation face eastwards - towards the rising sun, and the floor plan mimics the shape of a cross. However, both of these things are generally a result of the religious beliefs of christians, and developed a period of time.
This forms the apex of the church, the focal point and it is usually topped with a spire, or dome. Internally this area is marked out by large columns required to bear the weight of the tall structure. The shorter arms either side of this are known as Transepts and form the symbolism of the cross. These are often dedicated to particular saints with separate chapels or dedicated to particular aspects of the life of Christ - such as the Nativity (as can be seen in the Sagrada Familia in Barcelona). The Florence Cathedral does not have a Choir behind the Crossing, instead just terminating in an Apse. This is a semi circular ending, and in this case both Transepts also terminate in Apses.
We do know that plans of many religious buildings contain within them combinations of simple geometry. Often referred to as sacred geometry, the more complex the interaction and layering of such geometry, the more complex the overall building. Indeed, golden and geometric ratios were often employed in Greek and Roman architecture. This combination of ratios helps to give buildings such as the Florence Cathedral a sense of proportion - even though stands as the biggest building for miles! Whilst we can identify that a cross shape would not be part of a 40K ecclesiarchal building, other structural elements such as the Nave and Aisles can be quite at home, as can a number of chapels, each dedicated to different saints. This is because we know that although worship is centred on the Emperor, we also know that there are a number of saints which may also be revered!
Using information such as this we can not only be guided as to how a shrine or church might look in the 40K universe, but also get some understanding of what might be inside of it. For me, this is important in order to help create a believable piece of terrain. Anyway, I'm sure that this is quite enough jabbering from me.
If you are still interested, and I doubt by now you are, then some further and more detailed information can be found by reading here and other plans of churches can be found here.