For mine, the problem is that ship transfer, and in particular INSTANT ship transfer, significantly changes the way groups can concentrate forces, and not necessarily in a good way. Up to now, with no ship transfer, groups have to plan, coordinate and go to some effort in order to exert their collective influence on anything, be that dominating a system, swamping a CG, ganking noobs in starter systems etc - simply because of the travel required in order to concentrate their forces.
Ship transfer, with a delay commensurate with actual travel time if the player conducted the transfer personally, in and of itself would have significantly changed the way such groups could concentrate forces as it is. It would be improved, but would still take some planning and coordination on the part of such groups. And any players in the affected systems, if they picked up on the force concentration soon enough (by noticing the increased traffic and appearance of certain vessel types and groups), would still have time to 'get outta dodge', whether that be shifting system or play mode.
Now, however, with instant ship transfer, groups will be able to concentrate forces far quicker that the galaxy size and travel distances should allow - simply travel in their long range taxis and then hey presto they have their whole fleet at their disposal. And before other players even know what's going on, they face an armada that should actually have taken some time to concentrate. I fear that Frontier have made a snap call on instant transfer for the sake of something like CG participation but have neglected to consider how this will be used by various groups to exert dominance over others like never before. Ship transfer alone, with a delay, would have changed that dynamic anyway, but instant ship transfer, I fear, will go too far. If anything it will shift the balance of power in favour of groups that want to (unrealistically) quickly seek to dominate systems and CGs and the like with a minimum of coordination and effort compared to what they have to do at present. And what will the result of that be? Even more players leaving open, I fear, because the balance will have shifted further away from what the heart of Elite has always been - a lone pilot in his ship, trying to make his way in the galaxy and survive.
That's where I see the balance issue being - the way in which instant ship transfer dramatically affects force concentration beyond what simple ship transfer (with a delay) would have done.
This summarizes down to "makes it easier for people to do things together".
The negative slant just comes from the example you picked, positive examples exist too.