They are hiding the ship from the Shadows as they don't want to give it back. They want to take it apart and study it and make living death ships for Earth(and they do.....)
A Solar System is more then big enough for two ships. It can make sense for lots of reasons, like you have them hide in pairs. And the Sol system was a good ''out of the way place'' 1,000 years ago.
B5 is not a ''Sub''. It's a Space Station full...full...of traders, merchants and travelers. And Earth is only a Two Day jump, so that is ''not too far''. And, we'd assume ''other places that have human colonies'' might be even closer then ''two days''. So, Trader Bob goes to Wal Mart in Earthspace and buys a dozen eggs(using 2017 money here) for 99 cents (my Wal Mart has then a 38 cents) as he is All Ready heading to B5 on a ''normal trade duty'' for Intergalactic UPS or is just a cool, independent Space Trucker. So sure, after his ''long and hard two day trip'' he wants to mark up the eggs to make some money. So big deal, he sells a dozen eggs for $5.99. Well if your ''trapped'' on B5, and you want eggs, you pay the ''5 credits'' or whatever and buy them. It's like when it's Sunday Night and everything is closed, but you want mustard on your hot dog...you go to the only place that is open: The Quick-E-Mart and pay $5 for a bottle of mustard. Or like the people that live in Alaska or Hawaii and how they pay more for stuff...but it is not like they can never get fresh food in those places.
Wonder what they based it all on?
Well, even B5 does the ''This is Captain John Smith of the EAS Zeus'' most of the time.....
This is way too Real Life for a TV show. But they sure did this a lot on Battlestar Glatactia.