I'm not sure where the issue/limitation lies, but the AE autocraft system always requests the specific circuit that is in the recipe even if an ore dictionary equivalent is available.(With substitutions option on.)

For example:
The 4k ME Storage Component can be crafted with an Electronic Processor, but also with a microcircuit. If the AE system has an autocraft recipe that includes an Electronic Processor, but only microcircuits are available, the system will not craft and request an Electronic Processor be made available.

Consequences:
Every time the player gains access to new circuits all, still relevant, autocraft recipes have to be manually updated. A time consuming and annoying process.

That's actually not the case.

AE2 substitutions on will use but not craft equivalent items that already exist in your system. It is only possible for it to request crafts for the exact item you have in the recipe. This is an intrinsic behavior of AE2 that we have no control over.

The workaround is to prestock circuits of the needed tier using a system like level emitters on dedicated crafting machines. Prestocking is a good idea for the most common tier components, as well as things like ingots that take a long time to produce in the Electronic Blast Furnace.

The reason for this is the, data that is added via the pack custom recipes, the "This is the final 18th tier 99 circuit" blah blah blah

It screws with the Ore dictionary entry for the item, so it's considered a 1-off item instead of being in the dictionary.