It makes perfect sense actually. There is a difference between being hurt and being injured. Just like there is a difference between being sore and being in pain. If this is the regular Season his ramp up for recovery is slowed down. If they were concerned him running could further worsen an injury he would not be running and he would be shut down.
Him being sore running the bases isn't a massive concern... coming off a knee injury its expected. If he was going to compromise team performance he wouldn't be playing. If he was injured he wouldn't be playing. Its if they can be healthy enough to perform is the question and the answer appears to be yes but we will find out for sure tomorrow.