Do breeding items such as medallions and stained glass cause the resulting foals to be weaker where the item boosted them? (Ie do they tend to throw offspring weak where the item boosted them)

It's all random factor even seems can flop a foal

In general no the foal is stronger not weaker.

The medallion/glass boost is inheritable, so the foal should be stronger and better at breeding that feature.

However the random factor still does mess things up, just like real life.

I am so glad I am not a breeder in real life, it must tear you apart.

This is what I wondering if it was inheritable. Ironically I have a handful of broodmares and train for a living so I am all too familiar with real life "rf" haha. Although it's a lot more nuanced in real life as training/management/personality plays a much larger role that would be impossible to replicate in a game.