The explanation behind what I am about to say is going to make sense to some and be utter dreck to others. The reason it will be so widely interpreted is because we are dealing with fictional situations and one cannot look up an authoritative answer to the crucial question of 'How long does it take to turn 180 degrees and climb back to cruising speed?' If your answer to that is 'an insignificant amount of time,' then my arguments do not apply. If your answer to that is 'a significant amount of time,' then you probably already understand.
Typically, it works like this... you see someone (attacker) coming and you (defender) head toward them to cut them off. You do this because you are superior to them and it is a good day for a victory. If they change course, you change course and unless they turn around, you will meet more or less head on. This is where it gets interesting. If you can turn on a dime and maintain contact, you will have a battle. If you cannot turn on a dime and maintain contact, there will be a full salvo (or two) and then they will continue to their target and you will be out of position. It depends on your ability to turn and maintain speed.
Or...
As you sally forth to fight in the vast reaches of space, just before you meet them, they turn and you follow laterally. Then, after a little while, a smaller fleet comes in from the other direction and pounds whatever you were defending and there is nothing you can do about it since you are just a little too far away. So a numerically equal fleet split in two can wreak havoc on you and escape with almost zero casualties.
It may make sense to stay in your system until you are mounting an offensive of your own.
Of course this only applies to warp travel.
(I know you understand how the game works so that is not my point in the following.)
Hyperlanes are different. Once you begin the journey, you are committed. In that case, you would always await their arrival to defend. Unless of course you are retreating.
Worm hole travel is similar. Once you begin the journey, you are committed.
Does it really matter if the battle occurs in the space between the stars or near the edge of a system? I don't see how it has material impact on the outcome.
Interstellar travel without violating relativity is a staple of science fiction. These rationalizations have been used by Clarke, Heinlein, Niven, and Weber just to name a few.
If you don't like hyperlanes and warp stations, turn them off. It is one of the precious few things that are settable without modding.
I, for one, am glad that they are there. I fully intend to play a game with only the hyperlanes allowed and may even mod things so that the transit time is effectively zero. I plan to do this because Stellaris is the closest thing I have seen to Cole & Weber's Imperial Starfire and I am stoked!
I wouldn't be surprised if a lot of people would have been less likely to buy this game if it did not have these alternative movement styles. I know I would not have been as interested in it.
But again. What material impact is there on the outcome of a battle if it happens in deep space or merely on the edge of a system?
Maybe it would be better (and I think appropriate) to lobby for a buff to warp drive.
Having said all of that, I would add this. If movement of resources were discrete instead of abstract (i.e. convoys existed), I might be convinced that it mattered. I would certainly think that a warp race would be behind the 8 ball in a manner that knew no bounds. Perhaps this mechanic is in place to facilitate their ideas for an expansion or DLC.