So it is a very complex issue. Can taking a vaccine actually mess with an immune system that would otherwise fend off the disease? To what extent do we overgeneralize on the need for vaccination? When does it do more harm than good, and visa versa?

That's a lot of dollars worth of good questions. Unfortunately the water has gotten so muddied by other things that we may never know the answers with full confidence.

These water muddiers include:
1. Nationalism (our vaccine is better than yours)
2. Big pharma greed (leading to a fudging of the efficacy figures)
3. Narrative construction (a vaccine will be the world's saviour - also deflates the impetus to find out what caused the virus in the first place - not that there's any mainstream media interest in that anyway)

Correction: I mentioned that WIV was manipulating "harmless bat viruses" to make them more contagious to humans - although that's true - that wasn't the case with RaTG13, the closest known match to SARS nCov-2, which was kept at WIV, and appears to have not been harmless even in it's natural form.

There's an interesting article that traces RaTG13 to a Yunan cave and links it to a small outbreak in 2012 that killed several miners who were cleaning the cave of bat feces. The authors hypothesize that this virus, which was collected and stored at WIV, could have mutated in those that it infected - they lived for over 100 days - and may have been 'ready-to-go' without requiring manipulation. The virus was considered non-extant in nature, so it's source would still be an escape from an Wuhan lab, but it may not have required any additional engineering.

I'll try to look at this and other hypothesis in more detail in a different thread but just wanted to make the correction here.