The X9000 has a multi PL option that unfortunately is limited to 16 slots, at least in the 128 channel firmware. Being able to select "PL" on the fly for a low band radio would be an improvement. Also in 6 meters the repeater splits vary depending upon region, state, etc. You can fudge two splits per repeater output channel using the direct mode button, however there are easily 4 different repeater splits in the US plus oddballs.
Then there are the option code bits. I am using DES-XL ( on the bench now) for future Part 90 station. The option bit controls the Securenet board installed on the personality board. Likewise there are option bits for Extender noise blanker, Scan, Talk back scan, Direct mode (simplex) , VRS control, MDC and DTMF encode/decode, single tone, MPL and Siren, etc if so inclined. As far as I can tell no I/O control is supported in the radio other than horn/lights activation.
edit: as far as form factor. An external box would not be objectionable if it can minimize the modifications to the radio. Also there would be less concern about EMI from the new circuits directly radiating into the receiver. The only drawback is availability of mating plugs, however a scrapped control cable from a radio, siren unit etc, can be put to use. edit 2: Also an external interface will make it easy to support spare drawer units for troubleshooting/repair and even facilitate multiple radio control.
RFI-EMI-GUY