Hi tsialex,
Thank you for all your contributions to the Mac community! Perhaps my ROMs be of use.
I have multiple EFI-booting installs (Mac, Windows, Linux) and CSM-booting installs (Windows, Linux).
I got the machines used a few years back and both had FW 84 and upgraded processors from stock (W3565, W3670). One is a 4,1 -> 5,1 upgrade, the other a 5,1. Both are now running x5680s.
I upgraded to 89 to run High Sierra / APFS and had saved the bins from each upgrade.
The 2010 would not boot EFI Windows 10 after the 89 update.
I did not attempt to boot EFI Windows 10 on the 2009 after the 2010 showed issues.
EFI Linux Mint 18.2 showed a screen before starting GRUB along the lines of "searching for APFS volumes" which was new with the 89 firmware on the 2010. I will try to get a screenshot of the exact message when it appears again and also see if it also occurs on the 2009.
I have been cautious with my Mac Pro's after seeing your findings and having to reinstall Windows. I am holding off on 138/140 & Mohave until I receive an MVC metal -capable graphics card and am confident my machines not having any corruptions.
Here are the results of the binwalk:
Toms-Mac-Miniesktop $ binwalk Mac\ Pro\ 2009\ FW\ 0084.bin
DECIMAL HEXADECIMAL DESCRIPTION
--------------------------------------------------------------------------------
0 0x0 UEFI PI firmware volume
16524 0x408C UEFI PI firmware volume
24972 0x618C CRC32 polynomial table, little endian
35787 0x8BCB mcrypt 2.2 encrypted data, algorithm: blowfish-448, mode: CBC, keymode: 8bit
49948 0xC31C UEFI PI firmware volume
524288 0x80000 UEFI PI firmware volume
540812 0x8408C UEFI PI firmware volume
549260 0x8618C CRC32 polynomial table, little endian
560075 0x88BCB mcrypt 2.2 encrypted data, algorithm: blowfish-448, mode: CBC, keymode: 8bit
574236 0x8C31C UEFI PI firmware volume
1048576 0x100000 UEFI PI firmware volume
1114112 0x110000 UEFI PI firmware volume
1183814 0x121046 Certificate in DER format (x509 v3), header length: 4, sequence length: 986
1249350 0x131046 Certificate in DER format (x509 v3), header length: 4, sequence length: 986
1343538 0x148032 bzip2 compressed data, block size = 100k
1376256 0x150000 UEFI PI firmware volume
Toms-Mac-Miniesktop $ binwalk Mac\ Pro\ 2009\ FW\ 0089.bin
DECIMAL HEXADECIMAL DESCRIPTION
--------------------------------------------------------------------------------
0 0x0 UEFI PI firmware volume
16524 0x408C UEFI PI firmware volume
24972 0x618C CRC32 polynomial table, little endian
35787 0x8BCB mcrypt 2.2 encrypted data, algorithm: blowfish-448, mode: CBC, keymode: 8bit
49948 0xC31C UEFI PI firmware volume
524288 0x80000 UEFI PI firmware volume
540812 0x8408C UEFI PI firmware volume
549260 0x8618C CRC32 polynomial table, little endian
560075 0x88BCB mcrypt 2.2 encrypted data, algorithm: blowfish-448, mode: CBC, keymode: 8bit
574236 0x8C31C UEFI PI firmware volume
1048576 0x100000 UEFI PI firmware volume
1114112 0x110000 UEFI PI firmware volume
1183814 0x121046 Certificate in DER format (x509 v3), header length: 4, sequence length: 986
1343538 0x148032 bzip2 compressed data, block size = 100k
1376256 0x150000 UEFI PI firmware volume
Toms-Mac-Miniesktop $ binwalk Mac\ Pro\ 2010\ 0084\ RomDump.bin
DECIMAL HEXADECIMAL DESCRIPTION
--------------------------------------------------------------------------------
0 0x0 UEFI PI firmware volume
16524 0x408C UEFI PI firmware volume
24972 0x618C CRC32 polynomial table, little endian
35787 0x8BCB mcrypt 2.2 encrypted data, algorithm: blowfish-448, mode: CBC, keymode: 8bit
49948 0xC31C UEFI PI firmware volume
524288 0x80000 UEFI PI firmware volume
540812 0x8408C UEFI PI firmware volume
549260 0x8618C CRC32 polynomial table, little endian
560075 0x88BCB mcrypt 2.2 encrypted data, algorithm: blowfish-448, mode: CBC, keymode: 8bit
574236 0x8C31C UEFI PI firmware volume
1048576 0x100000 UEFI PI firmware volume
1114112 0x110000 UEFI PI firmware volume
1191555 0x122E83 Certificate in DER format (x509 v3), header length: 4, sequence length: 986
1257091 0x132E83 Certificate in DER format (x509 v3), header length: 4, sequence length: 986
1343511 0x148017 bzip2 compressed data, block size = 100k
1376256 0x150000 UEFI PI firmware volume
Toms-Mac-Miniesktop $ binwalk Mac\ Pro\ 2010\ 0089\ RomDump.bin
DECIMAL HEXADECIMAL DESCRIPTION
--------------------------------------------------------------------------------
0 0x0 UEFI PI firmware volume
16524 0x408C UEFI PI firmware volume
24972 0x618C CRC32 polynomial table, little endian
35787 0x8BCB mcrypt 2.2 encrypted data, algorithm: blowfish-448, mode: CBC, keymode: 8bit
49948 0xC31C UEFI PI firmware volume
524288 0x80000 UEFI PI firmware volume
540812 0x8408C UEFI PI firmware volume
549260 0x8618C CRC32 polynomial table, little endian
560075 0x88BCB mcrypt 2.2 encrypted data, algorithm: blowfish-448, mode: CBC, keymode: 8bit
574236 0x8C31C UEFI PI firmware volume
1048576 0x100000 UEFI PI firmware volume
1114112 0x110000 UEFI PI firmware volume
1188789 0x1223B5 Certificate in DER format (x509 v3), header length: 4, sequence length: 986
1254325 0x1323B5 Certificate in DER format (x509 v3), header length: 4, sequence length: 986
1343511 0x148017 bzip2 compressed data, block size = 100k
1376256 0x150000 UEFI PI firmware volume