I'm sorry but it sounds like your LBS is talking utter cobblers. Having a look at the Shimano specs for the Cues crankset you can clearly see it is suitable for 68 or 74 mm bottom bracket widths.
If you have a 68mm BB, then you just space it out, this has been standard for the last 20 years or more. It's not a bodge at all and recommended by Shimano themselves. As for creaks and increasing the chance of failure, what rubbish, i expect that there's a lot of folk on here that have spacers on their BB's to accommodate the crankset. I had a a MTB triple chainset on my old Dawes Super Galaxy and that was spaced out as standard from the factory, I rode thousands of miles on that bike with no problems.
The only other issue I could see was with the chainline, but CUES has a standard 50mm chainline, so again, no issues there. I really don't see what the issue is with fitting it to your bike.
Shimano CUES chainset Specs:
https://bike.shimano.com/en-EU/product/component/cues-u8000/FC-U8000-1.html