I'm not sure I understand what the concern here is. Bear with me though.
I like the 'Empire of Islands' analogy, it's quite apropo... and a strategy I also use heavily. There already are two mechanics built into the base game to deal with waves on islands and still have multi-point ingress to your primary cluster. Warp gate removal (and Warp Guardian) and Jamming Command Centers. These, for an additional 5-30 AIP or significant K, will keep all waves from attacking any particular island.
I don't believe that if you're not willing to spend the AIP/K to remove the threat to these islands that you should be able to consider them wave-defensable. I just don't, that's a main construction of the game. Either move your whipping boy or deal with the consequences. If 2/3s of a CPA wants your Fact IV and it's way off in Nowhere, Kansas... well... that's just gonna suck for you. You've already got your 10 minute warning for those actually. Time to triage what you really need to defend.
There are only a few places where I personally believe multiple ingress wave defenses should be viable, and the tactics I currently use to help deal with them on NON 10/10... I actually do play those, 10/10 is a special case and that's my usual AAR. I don't always like playing a game at 80 AIP the entire time, it feels like you're in a straight jacket on occassion.
1) Multiple exposed wave points off the primary cluster. This is not uncommon unless you're HIGHLY selective in your map selection. 2/3 choke points into the main cluster (and a nerfing of any left behind warp gates) is quite common. Since you usually have to have reasonable defenses at all chokes anyway to deal with threat, wave defenses here are not an outrageous idea.
My usual defenses consist of my MK I units on redirection patrol between all the chokes, so they 'eventually' get to the fight to support the turret balls. I'll usually end up with a static Riot II under glass near the entry (2 if only two chokes) for shutdown, and thus a portion of my fleet is usually involved in defenses. This is another case of warp gates ending up useless to me for fleet/star ships because of the need to have defenders autobuild but also to be able to construct the fighting fleet as well.
2) Mini-clusters. Some maps lend themselves towards taking over two or three smaller clusters on galactic edges. Homeworld as one, Fact IV and some fabs in another (and a nearby choke), and maybe a nice staging area that's easily defended near the AI homeworlds in a third.
Usually one of these areas contains a Dyson or a Rebelling colony for me. Because of this, I have pre-built fleet defenders. But these are optional events to the main game and should not be considered core play. Rebels are the shock troops of my forces and can get roughly anywhere quickly to help defend. Dysons are just brutal. In either case though you need a good volume of turreting just to drifter defend as the threatballs go wherever. Since your turrets are already there, wave defenses are viable ideas for these locations.
Usually I try to keep the star-lanes between these locations as open as possible for my fleet. All WHGPs removed, All Ions, etc. Only completely neutered systems on my 'highways' between the defense locations. You also want to try to keep a small set of transports available to 'high speed' yourself where you need to be, preferably stationed at wherever your fleet rebuilds from. Yes, they'll probably decay long before you get to the fight, but that's 4 systems they can get your units before everything slows down. Your turrets here are not defense, they're a delay. It requires a lot of micro to stay on the ball, and you won't always get there in time unless you don't run at the edge of your fleet's range.
These are the multiple ingress point wave defenses I consider viable strategy. You can control the waves, control them to your advantage and pay for it. There's one other but it's an edge case scenario, when you're parking on a coreworld and deflecting homeworld brutal results/defending a local asset, because you literally can't shut that warp gate down until end game.
The Empire of Islands, as Hearteater rightly pointed out, brings its own benefits in terms of lowered AIP and the like. I'll reiterate my stance here. I want enough defenses to be able to ignore small threats of drifters for any island so I don't have to fear freeing up 20-50 local threat as I pass through a sector of space and have to stop my fleet at every point to vacuum so it doesn't go haring off for that command center in the corner. Islands should not be able to survive in the late game against waves/CPAs without help.
The game is/was balanced around the idea of having a whipping boy or two. What is the re-balance in the removal of the MASSIVE amounts of AIP you're planning to avoid with this improvement? Yes, it's a nice to have, but it's also part of the game's challenge.
Your average planet has 3 connections. At 3 islands, that's 3 Warp Gates * 5 AIP = 45 AIP that would be avoided to not eat waves. What is the balance? Taking edge worlds to lower # of connections increases time to defend. There's balance there (accurate is up for debate) in the AIP vs. time debate. Keeping a hub safe is exponentially larger (to the point that they're abandonable to me) AIP to maintain wave defenses, particularly since it's hard to keep up wave defenses when 5+ wormholes can spew ships and you can't get your short-range firepower into play as efficiently.
The same argument for balance could be made about me wanting the ability to keep drifters off my lawn a bit easier, I agree. However, I don't want to avoid the pre-built balancing mechanics for CPAs, Exos, and AIP gain for defenses. If I never want to go near the target system again with the rest of my fleet, I'll never have drifters after a neutering of the surrounding planets. I need to see how the new SF plays out but I don't suspect they'd seriously hamper that. I just want... something... there so 20 fighters and a leech starship doesn't make my energy supply quake in its boots.