I also have relatively bad GERD and I've also noticed it getting better when I have flu or some other minor illness. I think this is just because I eat less and move less. Moving less helps because sometimes random movements in a wrong way can trigger the reflux.

GERD is also one of those ailments that seems to be sometimes cured by weird random lifestyle changes. Low/no carbohydrate diet is something some people swear by. I also know someone whose GERD was completely cured after an antibiotics treatment to an unrelated disease.

For GERD there seems to be one clear structural factor that has something to do with its development: hiatal hernia. However, the link is not perfect so it's possible other factors (such as some microbial imbalance) affect it too.