It sounds like there might be multiple factors to consider. If indeed you are experiencing some allergic/histamine responses in your training which is resulting in feeling more of a muscular burn, are you also seeing any changes in HR? Zones 1/2 should be consistently low-intensity; if they become too much in the M.E. realm then you’re changing the nature of the workout which will affect your training globally should it not be probably accounted for. If using poles for these workouts can help to mitigate that load and keep the effort low, then I’d say go for it. I’m a fan of using poles on steep and technical terrain anyway, so if you’re intending on using them for specific objectives then there’s a specificity benefit inherent in employing them now.
Hope that helps,