How did you retrieve the alkaloids from the limonene? Depending how you've done it, alkaloid profile should be the same as extracting with naphtha. Also, you can get white crystals with limonene if you take certain measures (if you have fumaric acid, it makes it much easier)
Even the same batch of DMT can lead to completely different trips, even in same dosage/setting. Also, specially if its been a while between batches, it also happens that your whole situation/set/setting changed, so independent of how you extracted, its possible that experiences also change.
I think when I extract with limonene and my pro, my conscience is somehow 'lighter' and this makes me go more at ease to the experience, and this could maybe have an effect in the experience. Some people might think the 'spirits' somehow preffer limonene but I dont need to resort to those sort of beliefs, I just prefer much more extracting with limonene because it smells so much better when extracting, its not shady to acquire, I love playing with fumarate precipitation on it, its not directly giving money to petrochem company and I know there will be no petrochem traces in my product.. That being said, I dont think its 'bad' to extract with naphtha, ive done it some times and had great trips and very nice products. Just lately tend to go to the limonene way. But each one has to decide according to his own preferences, availability of materials and cost, desire to experiment etc.