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I remember the modified trailer, it's pretty neat and wouldn't mind going that way too if I were to find one for free. I haven't thought that much about weather protection, but we do have a rain cover for the lift if required.
Your partner might be concerned with HousekittenHST being exposed to the rain on the Yepp in winter, but I can assure you that (here in Denmark at last) plenty of kids are transported on them in all manners of weather and seem to be doing just fine :-)
I've had my daughter on my Mini maxi since about 5 mouths old. At that stage she was able to hold her head up so I had her in a modified Halfords bike trailer cargo strapped to the deck. I went down this route as my partner to super paranoid about her being covered up if it rained. It's worked really well and she's been very happy in for trips over an hour, we've been on trips to my parents which is a 30 mile round trip.
She's 16 months old now so I'm about to invest in Thule Yepp Nexxt Maxi. I've got the bracket from Omnium which I'm going to have to modify to get it to fit, hopefully I'll get round to it this weekend.