Is there a way to modify a ps2/3 unit to only be in command mode?
No, because no modification is necessary. As long as a DCS engine sees the watchdog signal it will come up in command mode.
getting all units to start in command mode at the same time is only by luck. 1 out of ten always seems not to pay attention.
That's most likely because you're because you're exceeding the amp draw on a single TIU channel.
The "safe" limit for all DCS engines to always come up in command mode is not to give power to more that 6 engines on a single TIU channel. This will vary a bit depending upon what else on the channel is drawing power, e.g., several lighted passenger cars and cabooses.
This and a whole lot more is all in MTH’s “The DCS Companion 3rd Edition", available for purchase from many fine OGR advertisers and forum sponsors, or as an eBook or a printed book at MTH's web store!