I think your problem is automation, Adam...or the lack thereof. Jonesey told you the right info from the beginning in my opinion. When you eq something when solo'd up, you get a much different outcome once you add all the other instrumentation in. To me, that mix you posted up didn't seem bad at all. Maybe I'm just getting to be less of a stickler these days and only look for problem areas, but I had no problems with that mix until the end when the drums were alone.
Now, what I'd do if I were you? I'd automate on anything that needs to be alone on its own. If that song had the drums come in by themselves, I'd high pass that kick so that it wouldn't rumble as much by itself. I do this for every instrument in my mix when it makes a solo appearance. If a guitar sound of mine is all by itself to start a song, the eq will look one way. Once the song starts, the eq changes via automation so that the guitar sound fits with the mix and doesn't FIGHT with the mix.
As far as your comment about the company's making kicks/drums that work right out of the box.....I believe they have given people just that. Half of the mixes you hear on Youtube are mixes where people just used drum modules with little tweaks. If most of them had to mic up and record a real drum kit, they would fail miserably because the drum sounds of today are so good, no one can really totally fail by using one unless they ruin the sound with excessive compression or eq.
I too high pass just about every kick I have ever used UNLESS the kick just simply doesn't need it. I'm not one that messes with an eq extensively if the sound doesn't call for it. Especially when using these drum sounds of today. To me, they are SOO good coming out of the box, most home studio hobby guys would be lost if they had to actually dial in a real drum that wasn't recorded so good. See that's the thing...with these newer modules, the recordings of the samples are so good, the fail factor is so low, a person fails if they ruin the sound due to being clueless.
This is why programs like EZDrummer have done so well. They sound good and are affordable. BUT, because of those two things....everyone has the same/similar drum sound and they really haven't learned a thing about recording. Now you can even buy the kits people have assembled. How long before there's an automated bot that listens to your voice and creates the exact kit and sound you want? LOL!
The same for drum machine type sounds in my opinion. They already have a voice that is all their own. You either high pass it, or play around with the low end and then mess with some transient attack. If you recorded a real drum, you'd find that if you didn't get the recording right, you'd end up messing with more than just a high pass. You'd be messing with all the stuff in between as well and let me tell you, it's not very fun. These sounds we have today are a breeze to work with in my opinion. With little to no tweaking, it makes people sound like they are seasoned pro's. Heck, if you're successful with a drum module on a song, you can save all your settings and it's there for you every time. This won't work on a real kit because even if you took pictures of your mic placement and taped all your stands while writing everything down, tomorrow when you mic up again, it will sound different. So no template of eq's or compression will work right out of the box. But on these modules and drum machine sounds....brother, we have the world in our hands. :)
Just do the automation thing if you want something to play by itself, and then change the eq curve for when the instrument plays in a mix. This is how everyone else is doing it also. They don't just come up with one eq sound and go with it....they may have 3 different eq's for an instrument depending on what may be going on. But for sure, any time an instrument is by itself, it's a good idea to eq it for that "all alone sound". :) Good luck.
-Danny