An excellent question, and as one of the answerers on the linked Borg question, I agree that most of those reasons don't apply. These are largely speculation, but I can think of four possible explanations that fit with what we've seen of the larger universe:
1) Tradition
The Geth were created by the Quarians, and their appearance (basic humanoid form, etc) were clearly based on their creators, as most robots are. During the early phases of Geth creation, they likely shared equipment with their Quarian masters, and thus were designed to function efficiently with pilot-based craft.
The later Geth could simply be continuing this tradition, just like they continue to use humanoid physical constructs.
It's also worth noting that the Geth are shown to use non-Geth equipment, such as Legion's rifle. Maintaining a pilot-based system allows them to use the ships of other races when necessary (although this doesn't entirely explain why Geth-specific craft still use pilots).
2) Efficiency
We know that the Geth are capable of transferring from "platform" to "platform", and from our perspective, it can happen quite quickly. But from the Geth perspective, it may be tiresome, slow, or inefficient to move between hardware structures. (Picture the exasperation most humans feel when they have to move to a new home for work.)
It may simply be more efficient in a crisis to use a humanoid body to pilot a craft than to upload into the craft.
3) Safety
Put simply, ships blow up. If you are the ship, you might have a blackbox or something that could survive with your program stored on it, but it's very possible that the destruction of the ship would destroy you before you could "upload away."
It's likely a safer alternative to store yourself in a body that is contained within a shielded space, and equipped with an "eject" function. You may still be stuck in the void of space, but then all you'd have to do is wait for a passing Geth ship to come and download all surviving programs from the wreckage (likely a common Geth behavior after a battle).
4) Transportation
The Mass Effect universe is more like Star Trek than Star Wars, in that most battles aren't waged purely in space. Landing parties are common, and most major engagements include at least some surface component.
A Geth that uploaded into the ship directly would be stuck in the ship. A Geth running on a humanoid platform within the ship would have the option of landing and disembarking, something which we have at least one example (EDI with Dr Eva Coré's body) of an AI specifically mentioning as being an option they would like to have.
