FTA for S-Corp w/FTF and payroll penalties

Does the FTA apply to the 1120-S FTF penalty and 941 & 940 penalties separately?

For example, would a penalty on a 2017 940 affect the ability to apply the FTA for 2018 1120-S FTF? Or are each tax returns considered on their own?

Yes
Pick which one provides the most relief and use it there.