It's been a few years but it's pretty safe in all of central Padua. I also think it might be a little uphill from the train station to the tour hotel near the Basilica Saint Antonio. I was with my brother and SIL and we just took a quick taxi so no personal experience except from walking around Padua and back to the hotel.
I'm glad you are going early! I didn't and regretted it because there were lots of things I didn't get done. The botanical gardens are awesome. I probably would have booked a visit to the Scrovegni Chapel before the tour just because you only get 15 minutes in the chapel (and 15 minutes in a dehumidifying room before your visit) and that was not enough for me! This chapel is jaw dropping.
IF you are in to relics, be sure to see the relics of Saint Anthony in the Basilica - jawbone, vocal cords and tongue I think. Lots of relic opportunities this tour including St Catherine's finger (?) and head in Siena.
There is a forum friend who just finished this tour and they may have walked from the station. They are currently in France and I know she has had a long day today with another one tomorrow. I will message her to see if she can reply Monday or so unless others answer!