Liking it; couple of comments:
I do think the logo above the title is taking quite a lot of vertical space which is at a premium with an overlong description and several subcategories.
Since one of the advantages of the boxes layout is getting more categories visible without scrolling I think it would be very good to default to having the logo and title next to each other. Of course one could achieve this pretty much with css overrides but be nice to get it right by default.
On the grandchild category problem I do like your sub boxes but a possible optional setting would be to simply only show one level of subcategory with an indicator when a further level exists - maybe a “+N subcategories” in small text under the child category title if there are grandchildren.
And a masonry style layout would be ideal…