This is unfortunately still a limitation in what Keen has allowed in-game scripts to do: there's no way for TIM to look up the correct assembler blueprint to produce a given item, so the only way it can manage production of vanilla items is to hard-code all of the vanilla blueprints, which of course won't work for modded items. Eventually I'm hoping to make it possible to more easily provide TIM with additional definitions for modded items, but right now the only way to do that is to edit TIM's code, which isn't documented anywhere.

Would it be possible to have a dedicated assembler for a given modded component? Similar to what needed to happen in earlier versions of TIM? Or has that been removed from the coding?

It was removed to make room for the new scheme, so unfortunately there isn't room to support both ways at the moment. Hopefully eventually Keen will increase the script size limit.

I found out how to make the program auto craft modded components though Taleden may not like the fact that u have to moddify the code to do so but it is easy in all you need the component name and under the component list in the script copy the last line it (/Thrust,15,5%,,ThrustComponent) here is a line i added to the component list for Stargate mod (/largehydrogeninjector,1,1%) plus remember the the total percentage add up to 99% going over the percentage thing fer funky. Some component might need u to add the Component at the end like this one from Azimuth Complete Pack (/AzimuthSupercharger,10,1%,,AzimuthSuperchargerComponent) for the code to work correctly.
Sorry for this long discription but until keen let Taleden write code automatic to the quota custom data area we will have to manualy enter the mod componet information. So I hope i explained it enough to understand.