Publicly funded projects get conflicts of interest too.
My strategy is to let conflicting parties fight it out over round of publication. This has at least three major benefits:
1. It forces the conflicting parties to be open and release their data for scrutinization.
2. It tests the peer-review process, helping create improvements that benefit all peer reviewing.
3. It lead snarky journal articles, which are more fun to read.
I don't necessarily think the funding source means the study is invalid or corrupt, but I do think it should increase scrutiny and attention to replicability issues and so forth. It shapes the actual (as opposed to claimed) posterior a bit.
I had a colleague with this type of funding and I don't think there was any kind of quid pro quo or anything like that but I do think in the very least it increases pressure to file drawer unfavorable results to maintain funding.
Empirically speaking funding source matters though in the way you'd expect, in terms of interpreting results:
https://cdnsciencepub.com/doi/10.1139/apnm-2023-0594