Every time I hear people talking about internal Commlinks and Cyberdecks, I just picture Data from TNG.

The human skull has evolved to be a "skin tight" jar for your grey matter, and very little else. There's not a whole lot of room in there to fit a smartphone with a USB thumb drive sticking out of the side. And that is what we're talking about here, when they refer to "dongle".

We're not talking about a fleck of sand, we're talking about another component that adds a significant amount of function to your device. You're taking your ordinary smartphone, plugging in a Stealth Dongle, and turning it into a competitor for an Alienware laptop full of expensive hacking tools and software. That's going to require a little bit more room than a grain of rice.
Furthermore, I don't think internal implants come with access ports ala Star Trek unless you also invested in a Cyber Skull. That's why the book cautions against anything less than DR 5 being implanted. They cite security reasons, which means they want to avoid your cheap Commlink getting hacked and someone flooding your visual cortex with pop-up advertisements. If the implant were easy to get to, you wouldn't need to worry about security b/c you could just jam a finger in your ear and turn it off.
So... for my 2 cents, I don't think internal Commlinks can support Dongles. You opted to have it internalized for concealment and portability, the trade off is lack of customization and difficulty of repair. If it gets bricked, you'll need a Geek Squad surgeon to get in there and fix it for you.