We included the gym ME progression in the Big Vert plan because of the eccentric loading the jumps supply. we’ve found this has a powerful training stimulus for both uphill but maybe more importantly downhill running. This stuff will make your legs much more fatigue resistant overall.
All that said, though, if your toe is a problem then yes by all means DO NOT INJURE IT! Injury should be avoided at all costs. With an incline trainer you can get a serious steep ME workout carrying a weight pack.
Good luck with your training.