"...Do you try to account for the evaporation?..."
Yes, I do. That's the only way to get consistent, repeatable results with my recipes. I also cover my containers to reduce evaporation of the water phase and to keep my ingredients as clean as possible. I'd say a loss of about 25% due to evaporation alone is unusually high, so you might want to look into what's going on with your process to reduce that. My evaporation loss is maybe 1% or so, to give you some perspective.
I have compensated for evaporation in two ways -- first like Elmtree does (just adding a separate amount of water after heat-n-hold). The second way is by measuring out a slight bit more water than the recipe calls for to account for most of the evaporation, doing my heat-n-hold, and then adding a gram or three more water at the end if the water phase is light. I've gotten enough experience that this second method works pretty well for me now.
I am one of those who prefers that my water phase should reach my target heat-n-hold temp. First to keep things as sanitary as possible. And second I want my lotion to not cool down too fast when I initially mix it together. To solve this problem, I use the microwave to quickly bring the water phase up to the heat-n-hold temp, then put that container in my water bath for the heat-n-hold time.
"...the oil phase is always quite a bit hotter than the water phase..."
What you're seeing is the difference between the "heat capacity" of water versus oil. Water simply needs more energy to warm up to a particular temperature than oil/emulsifier. Unless you heat-n-hold for a long enough time ... or add a little extra energy into your water phase up front ... the water phase ingredients might not ever get hot enough by the time you want to make the lotion.
Digression: That's one of the amazing reasons why our planet functions as well as it does -- the incredible ability of water to even out temperature fluctuations in our climate due to its high heat capacity.