Yeah, there's a few problems.
As for the 8.7ly drive thing, it's likely a retcon. Even if it was a typo, I don't think it matter; as mike pointed out, the problem with 8.7ly is that unless are problems with this drive over 7.7ly that are somehow insurmountable, you'd think 8.7ly drives would be everywhere by now; you have to imagine that most people who operate starships would love to have Stutterwarp with a range better than 7.7. There's likely been trillions of livres spent on this effort, ever since the 7.7ly limit was found to break the 7.7ly limit; the mobility advantage is simply too great for militaries.
As for the the 8.7ly drive, if you want to include it I'd really not make it cost so much or take more volume. We already know that a skilled human engineer (what ... who needs a human engineer in 2300?) can extend a Stutterwarp's range by carefully monitoring the charge build up on a coil. This task is baffling to me because 2300 is a much more technology-friendly game than vanilla Traveller is: If a human can do it, a computer can do it better by 2300.
It's likely in this case, that the Stutterwarp maximum has been creeping upwards (and perhaps there was a time in the past when the range was like 6.8ly) as technology in the form of better drives, better coils, and better software has allowed the stutterwarp coil to accrue its charge more and more evenly. The fact that in the basic rules an engineer can extend the range of a stutterwarp by task shows that the 7.7ly isn't a hard limit - it's probably the safety limit at the moment given the state of technology of coils, drive computers, and the software that runs it and that Stutterwarp nerds can regularly fool with the drives to get them better range. The important part is that this task doesn't require you to physically add hardware to your drive; it doesn't cost anything more to run a drive like this. You just need skilled engineers who know what they are doing. This suggests it's likely a software issue.
That civilian ships like the ISV-2 has it means that the military has had it longer; the advantages to longer range mean more for military ships, who don't take the straight line route between two systems (the so-called "sewage tube" in 2300 military terminology) but instead dogleg to change their vector to make interception more difficult (as well as to mask their origin in the case of systems that have neighboring systems within 7.7ly). I'd simply let the German and the ISV-2 have it as being on the cutting edge of civilian drive computer technology. You should likely give it to a few other new build civilian ships. Basically every military ship have it already; perhaps they're already edging up to 9ly. Meanwhile, older civilian ships might have lower than 7.7ly because they're using older drive components or older software; if a civilian ship never jumps more than 6.8ly (for instance) the owners may have never upgraded the systems as improvements came out.
However, the multiple stutterwarp drive setup on the Bayern is arguably worse, since it can allow a vastly increased range.
Bayern's multiple drive system isn't a big problem.
The limiting factor to Stutterwarp is the rarity of drive-grade Tantalum.
The Bayern literally has to get rid of one of its drives to go further than 7.7ly.
So canon-wise, that's the reason why it's not a big problem.
However, there's this 500-pound genre-breaking problem with this "solution" of why the Bayern isn't setting-breaking and the setting-breaking problem is inherent to 2300's own rules:
... there's detonation missiles that use stuttewarp. If Drive-Grade Tanatalum is so rare and precious, why are they knowingly throwing the stuff away in single-use missiles? Over the course of a single conflict, they likely threw away more Tantalum than a dozen Bayerns could use.
So knowing this, it doesn't make much sense. Any ship, particularly military, should have double drive arrangements. Even triple drive arrangements. Cost is obviously not much a deal to them if they're tossing away stutterwarp detonation lasers. In Bayern it's described as some jury-rigged thing that doesn't happen very often to offline a drive, eject the core, put in a new one, then get it started. But this solution has to have been thought of someone before; I find it hard to believe that Stutterwarp has been around so long in 2300 without anyone doing it in a past, particularly navies. And if people do it a lot, inevitably automatic and safer methods to get these drive swaps are going to be thought of...
