I am looking at one company that has utility owned 2500KVA transformers 5.3 %IMP 12.47KV Primary and 480v secondary. I have not been to the site yet. The one-line has a fused switch with a 3KA Class L fuse on the LV side with no MCCB or trip unit. This is a 66MVA system x/r=2.78. My calculations place the LV distribution system off the chart in AF danger and around a 10 second arc time before clearing the fuse.

Has anyone dealt with a system like this before?

That doesn't sound like anything out of the ordinary. One key piece of information that you are missing is what is the primary side protection? Is this why you are getting the 10 arc time? Values on the secondary of step down transformers many times yield extreme danger situations. What happens if you use a default arc time of 2 seconds? That seems to be an industry practice in many cases.

Primary Protection

McFlash you are correct. I forgot to mention the 200E HV fuses on the primary. I have not been around a lot of different systems but no switchgear with a MCCB seemed odd. The only protection being a 3000a fuse was something I have not seen yet. The 2 sec. AF hazard is 114 Cal/cm2 @18 in. on the load side of the 3Ka fuse. The system feeds a busway 480v 4 wire.
I know most HV-LV secondaries have high energy levels and understand that fact. Has most seen systems as this? Seems like a MCCB with a trip unit would be much safer. But I am sure the plant will not want to spend the money now to add a MCCB.
Any ideals on this system configuration. Leave alone, or suggest install of a MCCB with trips to reduce the hazard level maybe with a maintenance switch?
Should the company be concerned about plugging in a busplug in the busway at that high of an energy.

We have this same set-up at a few of our older facilities. We decided to leave them as they are for now. Our policy prohibits plugging in bus plugs into an energized busway.

MCCB = Molded Case Circuit Breaker

When you say MCCB do you mean a main breaker? I hope so or I am lost. If not, disregard everything I am about to say

Lots of paper mills have this same system, no mains, I am working with many of them in the Southeast US right now for arc flash mitigation. There are a few solutions to consider.

Yes you can add a 600V main to your existing line-up, I build matching line ups like this, you can add somehting like the AC PRO trip unit on your main with Quick Trip for arc flash reduction but that will only reduce the Ei for the rest of the switchgear it is protecting, you have the same Ei's on the main itself and the secondary of the transformer. So, not really the best option for you, unless you have deep pockets.

Play around with different MV fuse TCC's, some work better than others and in some cases can reduce your clearing time on the secondaries dramaticly.

You can add a mini VCB in the place where your MV fused are housed with relays sensing the secondary side of your transformer, basis to advanced relays can be used here, good solution if you only have <10 such switches.

You best bet would be to use remote (Wireless) racking and operators, we have operators to do just about anything wireless.