Not sure you and I see this quite identically, though we may.
To me, any ship entering the system needs to be directed to an Imperial port (incoming traffic from another system).
Now, that 'movement instruction' could be provided by an Imperial beacon, the SPA, the locals under agreement with the SPA/Imperium, etc. but that sort of direction needs applied and alerts generated if an entering vessel does not report to the directed location. (Even if there are mobile customs inspection vessels, you don't order such a boat to burn towards an incoming vessel without a good reason because it is time and fuel... when a radio call and perhaps a follow up reminder of the consequences of non-compliance could do the job)
Why? Well, I'm Trader Joe and I'm carrying thunderballs. I jump in, land on an outsystem moon that has a thriving little black market, offload my payload and leave in a system where the only traffic the Imperium cares about / oversees in some fashion is that headed to the mainworld starport.
I suspect (for the same sorts of reasons it evolved in our world) that most systems would have *multiple* Imperial-approved 'ports of entry' for goods, visitors, immigrants and refugees. Look at the US and Canada - both have 'International' ports (air and maritime) and others that are not but thus don't see major heavy tonnage traffic (and even if you are in a small vessel and enter those waters, you need to report to the authorities at least by comms and more if they require it). I suspect, in the Imperium, any planet that accepts visitors (not interdicted or xenophobic or whatever) and has a population digit 4+ and a port D+ would have some aspect of Imperial presence (C+ for sure). It might be an agreement with locals to apply Imperial law (with an audit agreement) where relevant or it might be a single SPA officer at the sleepy port all the way up to a full Customs House and/or an SPA run port. That could mean quite a few spaceports in a system have an SPA agreement or presence, however limited. The places that don't would be off limits to incoming vessels unless they had pre-clearance certification (if such thing exists) or unless they had been boarded an inspected.
I also think that in any system that has an Amber system classification or Red would have the potential to have the IN or another Imperial department running system control to help track and ensure that whatever gave an Amber classification is not exported and foreign actors do not interfere.
commerce protection. If the System Guard/System Defense Force also does
Yes, this is another solid economic argument for a System Guard. Now, a System Navy is also possible, but less desirable from an Imperial perspective as a sign of nationalism which can in the long run be a problem.
From my limited experience in the flight world, looking at the 'standardized' weather reports and advisories, their lack of true rigor in that 'standardization' and the odd cases they sometimes have to report on makes full machine processing a huge challenge. I was looking at developing an app that would let pilots of small planes or helicopters who have phone coverage to enter the airport list they care about at present, then have the app automatically scrape the weather sources and other notifications tagged with that airport identifier and report alerts based on configurable parameters (changes in atmo conditions, incoming storms, some key tags that might be attached).
You'll still want to scan the stuff manually at some point because enough odd scenarios and a less than complete standard can both contribute to machine parsing missing important details.