Tooling is covered by machine rate for the most part. Some jobs that eat tools I'll add that into jobs cost.
Buying specialized tool for a job I liken to tooling and fixtures...becomes part of the job. Example...one bore I found was only attainable with a Burnishing tool @ $500. While the tool is adjustable...it it only adjustable within .03 so becomes job specific especially as bore was not a nominal size.
If I buy something say like a Wobble head for Rotary Broaching at a 1k, the head becomes part of the machine tooling along with the broach used and not billed to customer.
So...it short the answer is "It Depends".