Custom build to do (nearly) everything...

ood point. Thanks
I’m thinking a blob of silicone sealant might be enough or perhaps some epoxy

I think that is the opposite of what's needed and water will still get in there. I hate to say this because I know this bike has been a long time coming and you're excited about it, but I'd get it fixed properly from the (another?) builder. Or I'd grind it off completely, paint it like you did the stem, then cover it with a frame protector and use a zip tie or an adhesive cable guide.

i respect the bike and I'm sure it will turn out well. I'm in he middle of working out the kinks for a new build myself. it's always frustrating when you need to correct the mistakes someone else won't, but in this case it's worth the effort.