Did you ask the homebuilder?

It sounds like you are building a tract home with a production builder.

Any change you want to make to their plan is going to cost you money, regardless of whether it's "less" expensive. Bottom line they charge you for it because they can.

It’s not a specific cost for changing a room to a garage bay. It’s a cost for a CHANGE.

If this were our municipality, it would require applications, new plans, amendments, approvals etc.

As the OP used the term "upgrade", it seems like this is a production home. It's likely the OP does not have plans or permits yet and is just making initial selections. The engineering etc. would already have been done for both options; the builder just put the premium price on the tandem garage. I could be wrong but it sounds likely.

Because they can. They hold the cards. That is true for every single thing that you want to change. It will cost you.

A few good reasons have already been given but there are some others I'll list.

A garage is required to be separated from the rest of the house with the addition of specific materials to prevent the spread of fire. HVAC ducting would need to be reconfigured removing the new garage area for the rest of the house, and the electrical wiring would need changed to what I would think is an Arc fault circuit in the original proposed office to a gfci circuit for the garage.

If a garage door is installed there's a thousand right there. Installation of a header for the garage door would also add an additional cost. Throw in what others have already stated and the increase in price is justified.

You may see a poster with a cartoon character handle after my post trying to discredit my comment and disrupt your thread. Please ignore him, he is what is referred to as a internet forum troll. Not completely stable with no first hand knowledge in any subject.

Given the heavier load of a vehicle on the 3rd garage floor (versus furniture and people walking around) the increased cost might reflect the need for additional reinforcement (thicker concrete, rebar, etc.).

More concrete and a garage door.