Most of the formats served by YouTube are already chunked, which means they can easily insert different chunks of video (ads, etc) at various points in the stream by changing the manifest. This is trivial, computationally. The complexity lies in building the mechanisms to make it work.
The non-chunked formats are only used by older devices, and are lower quality. Those would require re-encoding to change, but few users see them anyway, and those users probably don't adblock.