The Set RTS On Close option is controlled through bit 3 of byte 0 of the first DWORD of the ConfigData entry in the FTDIPORT.INF file. This is the same entry that contains the Baud rate table.
The first DWORD is shown in bold in the INF fragment below.
[FtdiPort232.NT.HW.AddReg]
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HKR,,"ConfigData",1,01,00,3F,3F,10,27,88,13,C4,09,E2,04,71,02,38,41,9C,80,4E,C0,34,00,1A,00,0D,00,06,40,03,80,00,00,D0,80
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Please note that this entry is byte-reversed, so MSB the DWORD reads 3F 3F 00 01 and the least significant bit is Bit 0. When disabled (RTS not set on close), the DWORD would read 3F 3F 00 01. When enabled (RTS set on close), the DWORD would read 3F 3F 00 09.
These values are held in the registry under this key:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Enum\FTDIBUS\{Device VID, PID and serial number}\0000\Device Parameters\ConfigData
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