Great question.
We did release a “preview” version of measurements V2 in our Logic 2 software which does support annotations, unfortunately we only released it for analog measurements. We plan to get back to this, but we don’t have plans to add annotation support to digital yet.
The more direct solution to this would be to write a C++ analyzer plugin instead, which can add little markers to any positions on the digital channel you like, such as the dots we add to the async serial analyzer, or the arrows we add to the clock edges for the I2C and SPI analyzers.
Technically this API supports Logic 1 and Logic 2, however the official examples now only support Logic 2. It would be pretty easy to back-port to Logic 1, as long as FrameV2 features are not used.
details here: https://support.saleae.com/saleae-api-and-sdk/protocol-analyzer-sdk