Selection of differential expressed genes
You can usually get away with FDR &lt; 0.1, but that's as high as you can go. This all presumes you're doing follow-up experiments of some sort, of course. I guess you could increase the FDR more, but you're then really increasing the odds that your follow-up experiments will fail. Obviously increasing the FDR will decrease the confidence in the results, it's called "false discovery rate" for a reason.
Yes, fold-change cut-offs are mostly useful when you need to prioritize hits further. Small changes are almost impossible to validate with less-sensitive methods (qPCR) and less likely to be biologically relevant.
You're just going to waste your time if you ignore FDR.


Remember that all thresholds are intended to increase the odds of success in follow-up experiments. If you have infinite time and resources then you can set these to whatever you want, but you have neither so you better prioritize reasonably.

It's likely that you have a large batch effect in your data, effect sizes in cancer tend to be much larger than this.