I've always tried to set feeder overcurrent settings based on the rating of the conductor rather than the feeder load current (but I've never had a substation that only has one feeder). If there are normally open ties, you want to be able to pick up load from additional feeders if necessary without worrying about trip setpoints. If you have something like 336 ACSR conductor leaving the station, then a 600 Amp pickup for the feeder would be appropriate.
Overcurrent settings should protect a transformer in the event of a fault, they should not be used in order to protect the transformer from overload. In the event that the transformer loading gets too great, make plans to upgrade the transformer - don't de-energize it and put your customers in the dark. If that transformer was loaded to 200% of its rating for an hour or so, it would have very little effect on its life expectancy (even less if the overload happens during the winter).
My prior utility, a rural cooperative, had installed fuses to 'protect' transformers at several substations. Its a terrible idea, but I inherited the situation. Often, only one fuse blows and 2/3rds of the substation's customers end up with 1/2 of their normal voltage. If you have the feeder breaker set to trip due to undervoltage (on any phase), it would help to protect your customers' equipment for such an event.
If you are forced to use 69 kV fuses, 100E seems appropriate for a 5 MVA transformer. You want some cushion to avoid blowing fuse due to inrush from an upline breaker operation. I've also seen such fuses melt well below their rating because of heating due to a bad connection where the fuse meets the jaws of the holder.