Well yeah, that's why I knew even way back then to choose a cam with more exhaust duration. And I know we still choose cam lobes based on some of this. And I know there are other benefits besides flow to a modern cylinder head design. Combustion chamber being high on the list.
But how much potential loss... 15-20? 30-50?
I know... it depends. Just spit balling thoughts.

Intake/exhaust flow ratio data is still very important.  Camshafts are ground around that.

With that being said, even with an "undesirable" header, the TFS is going to be way ahead of any factory LR or MR cylinder head, even with work done to them. 

AFR doesn’t make an FE head.

Trick Flow is the absolute best bang for the buck.  Will support 700 hp out of the box with no work.  Come assembled with quality parts including CHE valve guides, PAC springs, etc.

Will work on small bore blocks.

Cast in the good ole USA.

I have some A's out there with lots of miles at 550-585 HP.  No issues

Cylinder thickness needs to be enough, that number seems to be different with everyone, but A's are some of the worst for core shift, so have it mapped.  C's are usually the best

Where I really see issues are often #2 and #4 mains cracking at the main bolt holes and almost always caps loose in the registers. 

As Brent said, got to be diligent.  Pay for the sonic map, mag and pressure test and don't take shortcuts

I guess I am a glutton for punishment.
I have installed/removed headers on my Mustang multiple times over the years. 3 different brands (I dont remember the names except the current Hooker Super Comps)
First was removal of the TRI-Y style that was on it when I bought it in the mid-70's. I then installed a set when I rebuilt the engine since it had been sitting in an impound lot for 9 years with the hood off and intake stolen.
I had transmission problems and had that thing together and apart too many times...
Got frustrated and decided the fix was to convert the C6 to a top loader. Well dont you know those headers were auto only. So along came the Hookers. Had those on and off a few times. Last time to address gasket issues.
I found the sharp edges of the weld bead at the tubes readily cut the gaskets and caused premature leaks. I "engineered" a fix and they stayed on for a long time.
I think I put in all the bolts in every time. GT heads.
I did the "custom bent" trick, and also ground the box end of my special wrench to thin it out a bit. The special sauce was before installation I located the tight spots where the wrench really wouldnt fit and very lightly dimpled the tube around the bolt area so the modified box end would fit on and off the bolt for final stage tightening. This helped a lot, but it's still a pain... (see my previous post on avoiding doing it in the car)

Edit- I just remembered the second set were from an obsolete brand Casler or similar. They were a sub-brand of a better known manufacturer.