On-demand and dynamic autonomous crafting in Industrial Warehouses will be done through physical assembly lines.
This means that available crafts are not necessarily limited by patterns (as in AE2 and RS), but by configurations of machines. This will probably be the balancing factor to #1 if implemented. Think of it like the Industrial Foregoing Stonework Material Factory except much more dynamic with its choices in machines.
For a craft to be valid and able to be requested for on-demand crafting, it must start and end on the same assembly line.
This means that while one-machine assembly lines are possible (and for small crafts perfectly fine), crafts that require multiple steps to reach the end will not send steps to other assembly lines (unlike the behavior of AE2 and RS, which will craft in multiple machines to achieve a final result if patterns are provided).
In order to provide extra materials for an assembly line recipe, you can use a robotic arm as a step in crafting. Robotic arms will provide a dynamic n <= 64 items of a single type per arm when adjacent to a pallet with items.
This means, however, that certain logistical challenges arise when first setting assembly lines up, but do have solutions:
What about crafts that are just layered variants of the same machine? Am I really going to need to set up multiple assembly lines for variants of multiple crafting table steps? Initially, yes. This is done as incentive for the player to eventually craft a programmable logic controller with the Arbitrary Sequential Processing module, which when active on an assembly line with 2 robotic arms around the machine will place items that are not the final output of the crafting job on an alternate conveyor to be sent back into the assembly line.
What about crafts that require steps be done in other lines to be crafted on-demand and thus require AE2/RS-like functionality? I introduce the Assembly Composition Matrix, a machine that acts as a representation of an assembly line in a sense. If assembly lines are permutations of machines, the ACM allows assembly lines to be permutations of both machines and assembly lines themselves. This is a late-game (in terms of the mod) structure that enables the player to on-demand craft items of any given complexity provided the player has the materials and has set up an assembly line with ACMs of the proper configuration of assembly lines. To set up an ACM, attach an Instruction Receiver to the start of the assembly line that you would like to craft with, and attach an Instruction Transmitter to the ACM itself. After that, simply configure the ACM to select the correct assembly line to represent, and you are good to go! The Instruction Transmitter and Receiver have a radius of 8 blocks by default. As assembly lines output as pallets to forklifts normally, you'll need to direct materials to the ACM in order to bridge the assembly lines together (fun fact: this will get easier when combined with a future feature, but that's for post-1.0). Otherwise, ACMs act just like a piece in an assembly line. When an assembly line inputs into an ACM, that input will be taken out by a forklift and sent into the assembly line configured. When finished, a forklift at the output will send the given item back into the ACM to continue the processing of that material.
What if I need parallel processing? For machines that aren't like crafting tables, the solution is just to build more assembly lines. For machines that are like crafting tables, assembly lines actually can handle parallel processing well, but will round-robin between all simultaneous crafts. This means that when you start 3 crafting jobs and have only a single line available that handles 1-step crafting, the speed at which everything gets crafted is 1/n times the normal speed.