It is a common misconception that the genome is one vast integrated machine.
It's not how it works. A more accurate image would be one of a collection of recipes.
Every cell with chromosomes (every cell with a nucleus - (every nuclear cell)) has a complete copy of our DNA. That means that every nuclear cell contains a full set of genes for producing proteins and other products.
It is only in certain cells, in certain circumstances, that certain genes are needed to be transcribed (copied to RNA) and translated (copied to amino-acids to make proteins) so that these products are - um - produced.
This is done, not by addressing any specific DNA locations, but by substances being released that chemically interact with special DNA areas called promoters, wherever they happen to be in the DNA. This interaction begins the process of transcription and subsequent translation.
To pick up on the recipe analogy, it's as if a customer has arrived at a restaurant and ordered a soufflé. The waiter conveys the order to the kitchen. The chef calls it out, "Soufflé!" And wherever the soufflé cook happens to be, he or she hears the order being called out and cries, "Yes chef!" and proceeds to crack eggs.
The soufflé gets cooked and served up. In the same way, a DNA-specification of a product (the recipe) gets turned into the product itself. It doesn't matter where the specification is located.
"Syncytin" genes are a good illustration, showing that the position of a transcription unit is irrelevant to its working. Certain retroviruses - HIV is an example - are able to absorb their target cells together into one "super-cell" that contains all the nuclei thus far absorbed. They do this by way of their env (environment) proteins that allowed them to attach to and combine with their initially targeted cell. Certain placental mammals have endogenous retroviruses with env genes that act during pregnancy in exactly the same way, forming a "syncytial layer" as part of the placenta. But different syncytins from different endogenous retroviruses on different chromosomes are used by different placental lineages!
When retroviral genes are found in the same DNA locations in the genomes of different species, it is not because they have to be in the same special location in order to perform any function they may have. They are where they are because of endogenization in a common ancestor.