On some serial ports, DTR is used for flow control instead of RTS. The problem arises because ports like MiniDIN-8 only have 3 real status lines (for Macintosh compatibility, those are HSKi, HSKo, and GPi). The 8 pins are really only 6 signals, because RS-422 uses differential lines for transmit/receive. For RS-423 (mostly RS-232 compatible), those become single-ended, but the 2 other pins can't be freely repurposed.
Do the Indigo2 and Indy connect their serial port pins to the same pins of the Zilog SCC? It surprises me that they would act differently since the hardware is basically the same.
https://www.xrite.com/service-support/pi..._interface
(Insert a link to Inside Macintosh here when I have time to look for it)
DSR shouldn't be part of this, though. DSR is not really used for anything. To control a modem, the host uses DTR to force the modem to return to command mode, and the modem sends CD to tell the host it has a connection active. These states don't serve any purpose for null modem connections, so crossing DTR with DSR is not really what you want. It's more like crossing DTR+RTS with CTS.