1. You are comparing a 41.3mm dynamic to a pair of balanced armatures on bass duties. Dynamic speakers tend to develop a lot more bass than balanced armatures... which is why a lot of bass players (granted, that are prepared to spend the money) really stack up those balanced armatures in the lows. The UE900s have what I would call adequate low end and are less likely to distort if you start digging in. They aren't tuned to be out and out bass monsters). You may want to put an EQ in front of them and start rolling off some of the tops (subtractive EQ) so the IEM becomes more bass focused. For real bass junkies, you are realistically looking at getting a quad in the bass if you want to keep up with the HD25s. With regard to the boxy thing, that could be a 200Hz issue (try pulling that down if it's sounding too boxy) or it could be down to the IEMs themself and how you are perceiving the sound from them - IEMs generally suffer with less wide sound stage... the 64 Apex/Adel (for those that remember) trades a little isolation and bass response for a greater sense of width. If you have access to EQ, you will be able manipulate the sound to give you more of what I think you are striving for.
2. Generally, the failure rate on hitting a perfect fit is low. Ears are of all different shapes and sizes but the process of getting the impression is the same. If the acrylic is too thin and the result is a loose fit.. it has to be built up with more acrylic. If it's the other way around, its shaved down. Normally manufacturers have a 30 day window where you request a refit - and they'll work with you to get the fit right. It's not in their interest to leave somebody with a poor fitting IEM. I was talking to Paul from custom IEM about this on the stand at the bass show. He says that poor fitting monitors are very, very rare now... however, he does check each impression before it leaves so knows if it's up to scratch or not. For manufacturers that aren't using 3D printing and still doing the casting method, the preparation on the impression before making the mould is a skilled task. It has to be shaved down to size (so it looks like an IEM would) and then dipped in wax. This can oversize the mould ever so slightly.. so when it comes to the final polish of the iem, it takes some now how and experience to not go too far. With 3d modelling, all the cutting, shaving and smoothing are done inside the computer... so the results are very, very accurate. Some of the smaller operations are not into the realms of 3d printing yet... so you are putting a certain amount of trust in the people building your IEM... but as I said, these guys have to be accommodating when it comes customers needing to get a perfect fit.