I'm not sure what the issue is. For post-boil gravity, that is a function of boil off (not time), but the IBUs are a function of time and temperature. I can't reproduce this with my equipment set up and recipes, as they are fine with preboil SG and OG.
If you change the batch from "kettle" to "fermenter" does anything change? That's a hint that something is off... because a recipe formulated for "ending fermenter" would include kettle losses. For example, you have "5.5 gallons" in there as kettle because you have 0.5 gallons of loss transferring to fermenter. But say you toggle to "fermenter"... that would include your equipment kettle loss of 0.5 so the actual ending kettle is now "6 gallons" which translates to 5.5 into the fermenter. You went from 5.5g to 6g in the kettle but did not adjust any grains... your OG and IBU should change due to the extra half gallon of water present. This should cause you to add grains/hops to account for the extra 1/2 gallon of wort you'll be losing. We're not calculating the recipe according to 5 gallons in the fermenter, we're calculating the recipe according to the total volume of water left before transfer, then the BH efficiency numbers would change as you lose wort going to the fermenter.
... maybe another way to explain, if you have 5g in the kettle and toggle it to "fermenter" nothing changes. If i read your recipe as "5g in fermenter" i would make sure my pre-boil volume was enough to leave me with 5.5g in the kettle so i'd have 5g in the fermenter. Of course i'd check your equipment to see before brewing, but i'd want to translate the recipe that gives me the same OG wort and then adjust volumes so i get a full fermenter.
Another scenario... i have a pilsner that I decided to start boiling for 90 mins instead of 60. Adjusting this value doesn't do anything... I change boil time from 90 to 60 and pre-boil is the same volume because it's a static user-supplied value.
I also suspect the BH eff calc doesn't take into account the equipment profile settings... i added 20gallons of mash tun dead space and kettle space and my OG/IBU didn't change... i would assume my eff numbers would be negative and/or break if i'm brewing a 5 gallon batch and have 20gallons of dead space.
I love the interface.. it's great, but i think some works needs to be done to reliably use it for recipe formulation. When you generate a recipe you want software that accounts for the equipment losses and efficiencies. It works fine if you know your losses/settings and manage to find a combination that works. Eg, if i set it for 6.5 kettle and 78% eff it seems to match my old keggle setup fine for OG and IBU calcs. But when going to a new setup with 20g kettles and different losses the numbers were way off... i had to use another recipe software to get my bearings, then transfer the settings here... 6.5kettle with 85% eff works most of the time but IBU is slightly off. My new setup is getting between 85-90% mash eff and my old setup got closer to 80%.
It would be good if i could copy someone else's recipe and toggle the equipment profile over and get the same product in a glass. Eg, someone has a "5g into fermenter" recipe but dumps their kettle right into the ferm so they have a "5g kettle" value and a "6.2g pre-boil" due to their 1.2g boil off rate. When I copy this recipe and change equipment to my profile with 1.5g/h boil off and 1/2 kettle losses i'd see a "5.5g kettle" and "7g pre-boil" value to hit. We'd both get the same result out of the fermenter for a 5g batch.