If you ever spend crystals to refresh mod energy, you're doing mods wrong.
Refreshing the mod store only costs 15c. You only buy the ones showing +5 or +6 speed, but you generated 22 possibilities for those 15 crystals.
Those possibilities are ALSO much more likely to be higher rarity (blue, green, gold).
It is FAR more efficient to farm mods using fewer crystals and more credits, in part bc there's nothing else great to spend your credits on once you reach the endgame. If you have tons of credits, you can even buy rare but powerful combos that don't show speed to see if speed turns up. Things like a Blue Off set or CD set triangle with Crit Damage primary, Off% and CC% as the two visible secondaries. There's great synergy in that mod, so if you have credits to spare, you buy it. Does it always work out? No! Of course not. But farming mods in the challenges almost never works out -- the hit rate is terrible. -- and costs 3.33 times the number of crystals (which you care about) only saving you credits (which you don't).
Doing things this way also means you don't have to clear out your mods as often. If you buy mod energy, you get 7.5 mods per 50 crystal refresh, and they stay in your inventory until you do something about them, even though most of them, maybe all of them, are trash.
Meanwhile for 15 crystals you get 6 mods available with Episode Currency, 7-12 mods available with credits and the remainder available with Ship Credits. Even if you never buy any mod except with regular credits, you're still using 15c to generate as many or more possibilities as the mod challenges which cost you 50c for the energy to get 7.5.
And since you get instant feedback about which ones are worthwhile before you buy, you only add 0-3 (I average ~0.75) mods to your inventory per refresh.
It burns through credits, saves crystals, and reduces the busywork of purging your mod inventory. There's nothing not to like about this.