Aftermarket software should really never interfere with the factory programming tools. When an aftermarket company reprograms the ECM/TCM/etc, they utilize an OEM file as a base starting point. Nothing in the process of modifying the files should ever cause the OEM tool to not be able to communicate.
Most commonly there are other aftermarket parts (Edge module, Banks module, Stereo system that monitors CAN) on the truck that are causing CAN communication issues. Either that or the dealer does not know how to use their IDS (or it needs an update).
As far as I know, you cannot use the IDS to modify or turn off the TPMS thresholds. There was at one point a long time ago that they did allow this, but FOMOCO has since had it removed from the IDS software.
Also, a little info on updating ECM or TCM software. When H&S products are installed on your vehicle, we use a generic base calibration file. This tuning file will NOT be the latest from Ford and it WILL overwrite any updated files that you currently have on the ECM or TCM. The only way you could get the updated TCM file and keep it while running an H&S product is to install the H&S tuning and select "NO" when prompted about transmission tuning. There are many reasons that the aftermarket is forced to use specific base tuning files instead of tuning every tuning file. The most logical is simply that it is nearly impossible to keep up with all the files Ford has released. Currently on the 11-14 Power Stroke we have knowledge of around 340 calibration files. To attempt to maintain a full database off all of those files in a tuned format would be an astronomical amount of maintenance.