@dale.robinson thanks for sharing your question here. I’m not sure I fully understand why the offset is needed. What exactly is the issue you’re trying to solve?
My understanding is that the “geoid offset” was thought as a way to get a local approximation of a geoid file. In that regard, PIX4Dmatic supports a list of most commonly used geoids, which would help ensure you have your Ground Control Points (GCPs) positioned exactly where they should be. If the geoid you’re looking for is not supported yet, please file a request here and we’ll see what we can do to support it.
In your comment, it seems there is some other vertical alignment issue between the images and the GCPs, this reminds me of this article when there is a misalignment between the two and a way to fix it which was thought for PIX4Dmapper: https://support.pix4d.com/hc/en-us/articles/206544136-Vertical-shift-between-the-model-and-the-GCPs-Cannot-mark-the-GCPs-in-the-rayCloud . The recommended fixes are different from the approach you suggest though.
If the same issue appears in PIX4Dmatic, there is the possibility to identify an image where a GCP is present, order the images in the image viewer by alphabetical order (click “…” in the image viewer > Sort by “A-Z”), find the image and start marking the GCP. Marking one should enable you to align the project to the right height and to easily mark the remaining set of GCPs.
Let me know if none of the above apply, looking forward to hearing more!