Please bear in mind that I have only read about 1/5 of this thread, consisting of the beginning and end portions, so if I ramble about something covered in the middle, I apologize beforehand.
I love the thinking around the secrecy of the PHALANX project. The manufacturing of conventional arms is an issue which greatly irked me while playing. The issue with secrecy and equipment availability seems to me less of an issue for the organization as a whole, however, and more of a regional matter, to be handled on a regional basis. I do notice that many of the conventional arms are associated with a specific region, if not a specific country, and it would stand to reason that bases in those areas would have more supply available for purchase. For example, the SMG is Chinese, correct? Then Asian bases would likely have more available, while South American bases would had more trouble acquiring them.
Another matter would be transportation. As it is now, purchased arms appear in base instantly. While this works for the sake of expedience, I do hope it will be changed down the road. I remember X-COM Apocalypse addressed this, but delivery times in that game were capped at 5 minutes. On a global scale, I would assume deliveries could take hours, depending on location.
With regards to the impact of the deliveries themselves, shipping visibility could be turned into a game mechanic. Whenever a player makes a purchase, the armaments need to be transported to base. Once the presence of PHALANX becomes known to the Aliens, they would obviously start looking for bases, and detecting/following supply vehicles could be one such method (as well as whatever, if any, espionage methods the Aliens may pursue). However, as shevegen pointed out, the media would likely pose a bigger detection risk than direct Alien surveillance. Thus rare, single shipments would entail relatively little risk, as I can't see the equipment for one relatively small force taking more than one or two trucks, plus protection (against human raiders, not Aliens). Repeated shipments, especially close together, would have a larger footprint. Also, there are the aircraft part shipments to consider, as they either fly in or are driven in, both of which have a larger footprint.
I have to run now. I was going to inflict more text upon you lot, but my time is exhausted for now...