Your ideas are intriguing, thanks for sharing. I greatly enjoyed mulling over the nuances of how they could work. I did hit some potential roadblocks for these ideas, though surprisingly while the first scenario is impacted badly, the second scenario actually benefits quite strongly from them.
1. Will motherships or at least Prime Motherships have a chase flag?
While thinking it through and misinterpreting your first idea as a defense-in-depth scheme for a bit, as opposed to a string of heavy warp camps in the traditional manner, it occurred to me that without a chase flag the strategy will depend entirely on AI threat logic. Waves become threat if the ships survive and threat logic avoids proportionately heavy warp camps until collectively they can take them on. The heavy warp camps will work but only as a deterrent and perhaps later as a speed bump if things go badly.
2. Somewhat related to number one, to my understanding when a ship disappears, in this case the mothership jumping out, it drops off the AI ships' target list, ie. they won't remember it or act on its last sighting.
I could be wrong but the only times AI ships seem to have chased my ships across a wormhole is when they were traveling the same direction for other reasons or were Special Forces or were part of event like in the Shard Retrieval missions in the Fallen Spire campaign. If I'm right that this is how it works in Classic, it brings up an interesting point in AI Wars II on weather cross-planet target tracking in a solar system or even between solar systems is feasible or desirable. Perhaps like a short term memory investigate last reported position or direction.
3. If a command station is present it will draw some of the wave aggression so not all of it will beeline for the mothership.
This one is perhaps not so detrimental but it does dilute the possible effectiveness a bit at least for the first scenario. However this is an asset in a delaying action / defense in depth spider planet setup for example as it takes some of the heat off the mothership and if the command station is destroyed before it leaves the mothership extends the value of the surviving turrets on its way out.
Your second scenario benefits from number three the same way and one and two allow the motherships to drop off the radar by jumping out. Additionally losing the command station could come with the added bonus that if you placed the command station in the middle of the planet the AI ships could potentially be half way only to either wormhole.
