There are platforms on which NULL, integer 0 and floating point 0 is not the same. Hence memsetting won't do the right thing. On modern platforms they are, but still, you don't want to get the Standard C Weenies on your back - they're even more annoying than the Rust Evangelism Strike Force. You don't want demons coming out of your nose, do you? :)
They do have a point, though. Suppose you are handling a struct you thought were memsetted but was not (your stupid team mate used those damn initializers!), then when serializing it you will get undefined bytes in the stream, possibly triggering hash values to mismatch causing mysterious rebuilds and other stuff.
Wrt to field accesses, yes those can overwrite padding bytes. Suppose a is an 8 bit char field, but padded to 4 bytes. Then "foo->a = 22" could be translated to "MOV [RSP+16], EAX" which overwrites the 3 padding bytes with undefined values. The solution, as you mention, is to use packed structs but in those field accesses are much less efficient.
Bottom line: code whichever way you want. :) Me, I like to live in the fast lane from time to time and those memset/cpy/cmp functions are sooo handy. :)