today's smartphones are all about the 'software stack,' not the 'radio stack,'
The referenced article is not exactly valid. The author is spouting off historical common-knowledge to hopefully gain literary credibility, and must lack the technical expertise to be authoritative on the topic... more about that later.
The entire point of the article is to say that Microsoft approves of Apple for suing other companies (both Nokia and HTC now) over software patents.
The systems in question (mobile devices with loads of integrated wireless technology) are a sort of fusion of tightly-coupled hardware and software. Essentially, the software part is a device driver, whether it's communicating with an RF frontend or reading bytes from a capacitive touchscreen (which is why Apple has no grounds to be suing anybody right now). Also, Apple originally denied licensing their touchscreen software to Nokia in the first place, so they are essentially monopolizing it.
What this boils down to, is that some things are patentable while others are not. The capacitive touchscreen design - the physical form, the novel arrangement of metals and plastics and capacitive material - is patentable. The RF Frontend is (potentially) patentable, novel dedicated circuits for decoding baseband information are patentable. Reading bytes from an N-pin connector and interpreting those bytes is not patentable.
Now, to address the 'radio stacks are trivial comment': although the baseband portion (i decline to use the term radio here) does use a large part of software, that concept is already quite old.
Software-defined-radio was originally designed back when certain radio technologies were still young and they needed an easily reconfigurable transceiver. Transceiver technology has had quite a bit of time to mature since then, and now that we are approaching the theoretical limit of wireless channel capacity, companies are turning toward dedicated silicon. Dedicated circuits have the benefit of increased speed as well as the benefit of decreased power consumption (all that and more!), when compared to a general purpose dsp. When it's economically viable for a company to produce a dedicated circuit, then they usually will, and they should seek a patent for that device.
The aforementioned dedicated circuits ARE patentable, but the software used to control them is NOT.