And as I am looking at all of this, please excuse my ignorance, would changes to the butterfly.c file have any affect on my circumstance where I am attempting to use the "linuxgpio" programmer?

Thanks!
I hope the maintainer of this project returns and takes care of our issues.
Do let me know if the patch worked for you! Fingers crossed.

I'd love to help, but I'm actually still quite busy reinventing the wheel and porting the whole thing to Swift, using ORSSerial Library.
Can't you switch to 6.3? OTOH, this patch would be quite easy to apply manually.
Just look for the corresponding section in butterfly.c (butterfly_set_addr).

Using a black-box (client-provided) which is connected via Ft232R USB adapter, most likely ancient boot loader, following AVROSP protocol (and working correctly with avrosp.exe).
My job here is to port a Windows Firmware Updater (using avrosp.exe) to Mac OS X.

ATXMega256A3 (might be -U, can't find out without disassembling the unit which I am clearly not supposed to do).

Due to NDA I cannot disclose any further details, but I can provide a partial serial log if you're interested.
I've analyzed serial communications and that's how I finally found out what is going wrong there.

For some reason, buffer size is reported as 0x0080 (128 bytes) and the update process fails, as 512 bytes (page size correctly given in avrdude.conf). are expected.

The even more serious problem, however, is that extended addressing is not being used by avrdude in this case.
"A" 0xff00" becomes "A" 0x0000 instead of "H" 0x010000", thus overwriting flash memory from the beginning instead of appending the code properly.

I have applied this (rough) patch, which makes it work; just wanted to let you know.
I probably can't use avrdude anyway, because of the restrictions GPL would impose.

Anyway, here's the patch:

--- butterfly.c.orig 2014-07-16 22:14:58.000000000 +0200
+++ butterfly.c 2017-05-23 22:49:20.000000000 +0200
@@ -321,6 +321,10 @@
   PDATA(pgm)->buffersize = (unsigned int)(unsigned char)c<<8;
   butterfly_recv(pgm, &c, 1);
   PDATA(pgm)->buffersize += (unsigned int)(unsigned char)c;
+
+  // overriding it for now
+  PDATA(pgm)->buffersize = 512;
+
   avrdude_message(MSG_INFO, "Programmer supports buffered memory access with buffersize=%i bytes.\n",
                   PDATA(pgm)->buffersize);
 
@@ -424,6 +428,7 @@
 
 static void butterfly_set_addr(PROGRAMMER * pgm, unsigned long addr)
 {
+if( addr < 0x10000 ) {
   char cmd[3];
 
   cmd[0] = 'A';
@@ -432,6 +437,19 @@
  
   butterfly_send(pgm, cmd, sizeof(cmd));
   butterfly_vfy_cmd_sent(pgm, "set addr");
+
+  } else {
+
+  char cmd[4];
+
+  cmd[0] = 'H';
+  cmd[1] = (addr >> 16) & 0xff;
+  cmd[2] = (addr >> 8) & 0xff;
+  cmd[3] = addr & 0xff;
+
+  butterfly_send(pgm, cmd, sizeof(cmd));
+  butterfly_vfy_cmd_sent(pgm, "set extaddr"); 
+  }
 }

Best regards,
Stephan