In order of likeliness, the paths would probably be 2, 3, 1.
If PHE follow usual UK public sector practice, at least your concerns could be registered in your exit interview, though the findings from that would most likely get buried in the bureaucracy. Then again, I was never high enough in the civil service to know what happens to exit interview notes.
As I said in my first post, faced with a similar situation twenty-five years ago, we eventually adopted a database solution (MS-Access!). But that position evolved over time. The question this whole affair raises to me is to what extent PHE’s IT team are at the current cutting edge of the industry. Given that they are a public sector organisation, I suspect that they do not have access to new kit, the latest thinking on software architectures, the time to go on training courses, or are in a position to recruit the brightest and best as their salary rates will not match those on offer in the wider industry. But this is the elephant in the room; it’s far easier to shoot the messenger. And hence your option 2.