I have dealt and still deal with lipomatosis also. Mine never get any bigger than about an inch or so in diameter, but they're still annoying to me, especially with a relatively low bf%.
For the past 15 years or so, I've researched options for combating/correcting this, but I've never found anything groundbreaking through my own research or from physicians.
At first, I had a military doctor cut out a couple of the largest ones that were in a joint area. And, like you, I didn't want scars all over, so I attempted a sort of mesotherapy under my own direction. I didn't realize any real gains from this, so since that time, I've opted for the only real cure/adjuct, superficial surgery.
I've gone to a plastic surgeon to have about 30 cut out at one time, and I've also cut out about 40 or more myself. It's a relatively simple operation and can leave only minimal scarring if your surgeon is skilled enough and you follow proper post-surgery care protocol. I'm not sure how much this type of surgery costs in the US, as I had mine done while in Stuttgart, Germany, so you'll have to do a little research.
Anyway, for me personally, I prefer the tiny scars to having small subcutaneous lumps by far. And as time has gone on, I've noticed that if I'm diligent about cutting out the complete capsule, the lipomas don't return in that same area. I get some new ones every now and then but the rate has significantly decreased over time.
Good luck in finding a solution that fits you.