I don't disagree with any of this. Definitely, part of the problem in my group was that certain players were only interested in combat.
However, imagine a case where the players are about to run afoul of an imperial customs frigate.
Of course they can decide to take on the Imperial Customs Frigate if they have the skill to do it and for some reason decide to. Granted there are campaign level ramifications for taking hostile military action on Imperial personnel and assets. Even the best of criminals don't operate like mad dogs. Mad dogs attract unwanted attention and get put down eventually. This is why crime syndicates tend to keep under the radar for the most part and bribe law enforcement instead of just wantonly slaughtering them.
If the players decide to make murderhobo decisions, they should face the consequences... unless you want to run a murderhobo game.
The way the game reads in the book is a game where the characters are going from job to job spending most of their money on repairs and upkeep while trying to stay a step ahead of the authorities. However in very short order their skills surpass that notion, which raises two questions for me: why are such skilled characters getting such a meager take on their work, or how did these guys get so far in the underworld so quickly? And as someone else said before, it's not just combat. In your example with the train, at that point the train is easy for the slicer to stop and the ace to pilot, the bomb is easy for the mechanic to disarm, the bomb is easy for the explorer to find, and the enemies are easy for the hired gun to kill. Our group played through Beyond the Rim, and whatever circumstance there was to complicate the narrative, someone in the group had no problem overcoming it in short order.
That is the default starting situation described in the book. You are not beholden to use it as many people have run all manner of campaigns that aren't that in the game's short )so far) lifespan. Success and positions of power are not just about who is the best skilled. It takes a mix of preparedness, skill and luck to achieve great things. If your players can leverage their skills properly and make the right contacts and are careful about the sorts of Obligation they accrue then they can work away from their hand-to-mouth beginnings.
The one thing I do agree is that the core book does not take any space to explain to new GMs the ramifications of the level of XP awards they hand out in this system. I imagine that the sudden power spikes might come as a surprise to GMs who aren't used to evaluating game impacts when they do their read through of the rules. Using the default XP awards, PCs stop being small stakes protagonists in a reasonably short amount of time. It can take some by surprise that ten sessions in the PCs suddenly lay waste to a crime cartel hit squad that the GM thought would have been more than a speed bump.
What are these campaign level ramifications you speak of? As the lowest common denominator of gamer, I'm afraid this is over my head. Could you be more condescending? It might help my understanding of how to better run these games.
Of course they can take on a customs frigate if they have the skills. Of course it will draw attention if they do. But then again it might not, because the slicer will just jam their transmissions and perhaps even reconfigure the ships' transponders.
None of that changes the fact that combat results in nothing like what we see in the movies, but rather something more like the Expendables laying waste to armies of thugs. Realistically (in the context of Star Wars), a group should think that engaging a superior force is a bad idea unless they have some situational advantages. The mechanics of this game encourage players to think otherwise and with good reason. I noticed this in my read through of the rules during the beta and after the game was released. I noticed it while playing as a player and as a GM.
Also, everything you're saying basically boils down to "they can do that, but there might be consequences." The long term consequences of a combat don't make playing through the combat itself any more interesting. The issue isn't about the circumstances or consequences of combat. The issue is about making the combat itself a more exciting and interesting part of the narrative of the game. Plenty of other games accomplish this much more effortlessly. As a fan of Star Wars and many of the mechanics in this system, I want to see this game do it too. I have a hard time believing that the developers didn't consider all this while they were making this game. Perhaps they should put some articles up on the main page with suggestions, examples, and how they keep the game (and in this case, combat encounters) interesting at high levels of experience.