Okay, here we are again.
Let's summarize the current status first.
We have the F4F where the panel cannot be damaged (alternatively: Cannot be damaged with a reasonable probability).
The suspicion expressed that this might have been caused by a "wrong" alpha channel of the panel textures turned out to be wrong, a dead end.
Evidence shows though that the F4F class code causing possible panel damage is suspicious:
if(s.startsWith("xxarmor"))
{
debuggunnery("Armor: Hit..");
if(s.endsWith("f1"))
{
if(getEnergyPastArmor((double)World.Rnd().nextFloat(8F, 12F) / (Math.abs(v1.x) + 0.0001D), shot) > 0.0F && point3d.y > -0.442D && point3d.y < 0.442D && point3d.z > 0.544D)
FM.AS.setCockpitState(shot.initiator, FM.AS.astateCockpitState | 0x40);
Ton414 followed my suggestion that this code part is wrong, he replaced it with parts of the F6F code, turning it into:
if(s.startsWith("xxarmor"))
{
debuggunnery("Armor: Hit..");
if(s.endsWith("f1"))
{
if(getEnergyPastArmor(point3d.y > -0.645D && point3d.y < 0.406D && point3d.z > 0.3D)
FM.AS.setCockpitState(shot.initiator, FM.AS.astateCockpitState | 0x40);
This, sorry to say, is bollocks too.
It still binds the panel damage to the wrong hitbox, and to make matters worse, puts the bullet location checks into a completely wrong spot.
It's questionable whether the armor plate can be hit at these coordinates at all.
Let's face the facts.
This is what the armor plate looks like, the part which is currently used by Stock IL-2 and by Ton's modification to check whether the panel was hit (the hitbox is the green dish):

Doesn't look to bad, eh?
Well... it does.
The problem is: This hitbox would only work when the plane is hit from the front, but then again, a bullet likely won't ever get there, since it would have to travel through all the hitboxes of the engine first. That's like real life: You can hardly shoot the panel to pieces when shooting at it from the front.
Why that?
Why can't I hit this hitbox from behind?
Because there's another big hitbox covering it (the big blue something):

(And to make matters worse, the green dish hitbox is bound to the "blister" mesh which is the moving part of the canopy, meaning that the hitbox moves aft when you open the canopy - fail!)
Looks weird?
Not really.
Let's take a look at the F6F comparison, a plane where the panel damage is known to work flawlessly.
The hitbox used for panel hits on the F6F looks like this (the big red something), note the similarity to our big blue something on the F4F:

Isn't that a tad too much of a hitbox just for the panel?
Nope, not when you take the additional coordinate checks in Java Code into account.
Applying them, this is what remains of the hitbox when it comes to panel hits:

Okay then, back to our big blue F4F hitbox. It's called "xcf1" (for the F6F the panel hitbox is "xcf3" but we don't have that on the F4F, "xcf1" is the equivalent):

Applying a few simple coordinate boundaries to it, we get this final reasonable, uncovered and unarmored hitbox:

The regarding mod is here:
https://www.mediafire.com/file/wxaxr4ua1kncyel/F4F_Hitbox_Fix_2017-02-06.7zIt works with all base game versions.
IL-2 4.09 Rebels need to have the "AircraftLH Stub Class Mod" installed (it's a mod that add's a "placeholder" AircraftLH class to close the gap for something that has been introduced with 4.10m).
If you don't have it yet, get it here:
AircraftLH "Stub" Class Mod for 4.09 Rebels only:
AircraftLH Stub Class Mod for 4.09m based games onlyThis should work for 4.08m as well (untested though).
Java Sourcecode can be found here:
https://www.mediafire.com/file/3nwatnobivhi0n9/F4F_Hitbox_Fix_Sources_2017-02-06.7zI've performed a couple of test sorties against A6M fighters and my panel did get damaged successfully now.
Best regards - Mike