There are a small number of ways that a planet behind a chokepoint can be a problem.
If enough ships build up there, some of the ships may attack other systems (border aggression). You can stop this by periodically clearing them out, or better yet by killing guardposts. The Bouncer AI type makes this easier to do. If you REALLY want a system to not accumulate ships, you can put turrets in it using a mobile builder. Keep an engineer or a minifort in there with them, plus a remains rebuilder, and the reinforcements will suicide into the turrets. You probably need Mark V turrets (and thus Core Turret Controllers, and thus Vengeance of the Machine enabled) for that strategy to work well.
Ships in the system could be pulled into CPAs. Same solution as above.
Waves and exos can spawn at warp gates. Kill all the warp gates (and eyes, and special forces guard posts, and anything else taht acts as a warp gate) behind your chokes.
If you can't establish chokes, you'll want Mark V turrets on any planets exposed to non-neutered enemy planets, if possible. Possibly miniforts, which are always available.
If you neuter everything behind your lines, neuter everything adjacent to your planets, and keep some defenses distributed around, you should only need to pull your fleet back for CPAs, counterattacks, and exos. CPAs don't happen that often, counterattacks are triggered, and exos are only there if you turn them on. So, you hopefully shouldn't have to shuttle your fleet around all that often.
It may be worth keeping a separate defensive fleet. Fast and especially teleporting ships are good for roaming defense.
Your ships move 2x as fast in friendly systems, and even faster than that if you have logistics command stations. Try to capture systems so that your fleet can get around mostly through friendly systems when defending.
Loading the slowest ships into transports is really helpful.