PDF's drawing model inherits from PostScript, which was originally designed in the early 80s. It works and is really nice but the one glaring hole it has is missing transparency support. The original PDF spec from 1993 has no transparency support either, it was added in version 1.4 that came out mere 8 years later in 2001.
Setting drawing operation colours in PDF is fairly straightforward. You list the values you want and call the color setting command, like this:1.0 0.1 0.4 rg % Sets RGB nonstroke colour
0.2 0.8 0.0 0.2 K % Sets CMYK stroke colour
The property name for alpha in PDF is CA and ca for stroking and nonstroking operations, respectively. This would imply that you should be able to do this:
0.2 CA % Sets stroke alpha? [no]
But of course you can't. Instead the alpha value can only be set via a Graphics State dictionary, which is a top level PDF object that you then need to create, use, link to the current page's used resources and all that jazz.
This works fine for use cases such as compositing layers that do not themselves use transparency. In that case you render the layer to a separate XObject, create a graphics dictionary with the given composition parameters, use it and then render the layer XObject. It does not work at all in pretty much any other case.
The more observant among you might have already noticed that you need to create a separate graphics state dictionary for every transparency value used in your document. If you are, say, a vector graphics application and allow artists to adjust the transparency for each object separately using a slider (as you should), then it means that you may easily have hundreds or thousands of different alpha values in your document. Which means that you need to create hundreds or thousands of different transparency graphics state dictionaries if you want to preserve document fidelity.
Why is it implemented like this?
As is common, we don't really know (or at least I don't). The Finger of Speculation points towards the most usual of suspects: backwards compatibility.
Suppose the alpha command had been added to the PDF spec. It would mean that trying to open documents with those commands in older PDF renderers would cause crashes due to unknown commands. Yes, even if the document had specified a newer minimum PDF version, because PDF renderers would try to open and show them anyway rather than popping an error message saying "Document version is too new". OTOH adding new entries to a graphics state dictionary is backwards compatible because the renderer would just ignore keys it does not understand. This renders the document as if no transparency had ever been defined. The output is not correct, but at least mostly correct. Sadly the same can't be done in the command stream because it is a structureless stream of tokens following The One True Way of RPN.
If the hypothesis above is true, then the inescapable conclusion is that no new commands can be added to the PDF command stream. Ever.