When I look to the Ixora schematic I see pull-down resistors (e.g. R3, R65, R88 for LEDs) but with the T30 module I can set internal pull-ups and pull-downs. I would like to understand why they are added.
Having the pull-resistors on the carrier board is a more generic solution. On the carrier board you know which function a certain pin is going to have (e.g. LED), therefore it’s possible to define the default state of such signals with a pull resistor. If we would do that on our modules, customers might have problem with their custom carrier boards as our default value from the module wouldn’t fit their requirements. Furthermore we might have different features on the same module pin on different carrier boards from Toradex (is mainly not the case of course, but potentially possible). If we would define the default state of a pin in software, it would only work on certain of our modules.
There is also a second reason. It could be possible, that some modules in the future might not have the possibility to set pull resistors in software. This means we would be in trouble in the future if we wouldn’t define the default state of some signals on the carrier boards.
The general rule is therefore: define the default state of your pins on the carrier board where you exactly know which feature you use on which pin and which default value you need to have.
Note: On Colibri this pull resistors might not be sufficient for critical signals which need to be in a defined state from the beginning (power up). Depending on the module and pin, there might be a short time where signals get driven from the module during boot-up. If you have critical signals which always need to have a defined state, you would have to do a hardware solution. E.g. a buffer circuit which gets enabled with nRESET_OUT from the Colibri module.
Since you are using the Apalis, this might not be an issue as you should use the POWER_ENABLE_MOCI signal to enable/power up the devices on the carrier board. More information can be found in the Apalis Carrier Boardd Design guide.