You're spreading misinformation.
1) The cross-rate initiative is part of "Sailor 2025" and generally need not apply to nukes. The reason it doesn't apply to nukes is because nuclear personnel go through a rigorous, specialized training and certification program. As a result, nukes need to do the job the Navy spent all that time training them to do. They have limited opportunity to pursue cross-rate qualifications, and the non-nukes aren't going to be permitted to help with nuclear watches, either.
Some examples of where the cross-rate initiative is being used in the submarine force: Yeoman qualifying broadband operator or electronic plots operator, torpedomen qualifying assistant fire control technician of the watch, etc. We did take a senior-in-rate qualified ETN and have him stand electronic plots operator last deployment, but it was because there literally were no other options. Despite that, were I in the CO's shoes I wouldn't have done it - it grossly puts the member at a disadvantage for his in-rate knowledge, professional development, and advancement to spend 8 hours every day drawing squares and plotting points on the fusion plot. Also, being able to do that in the first place was largely due to the VA class combination of RT and AEA into one watchstander, and the elimination of a throttleman, so you have a glut of wire rates on deployment who you either have to leave at home or find something productive for them to do because a 6-section watch rotation is not happening with the significantly fewer bunks on the VA class submarine.
2) For in-port watchstanding, MMs qualifying SEO might be a possibility, but with SVRLA batteries SEO only needs to be manned while production work or plant evolutions are occurring. MMs qualifying SRO will not happen, and I'm pretty sure there's some higher guidance that it's not even allowed. Quite honestly, if you show me a boat that can't man a 4 duty section with 3 watchsection SRO rotation while sending 1-2 people on leave or to school, then you're showing me a boat that is improperly managing its qualification program. Unfortunately there are a lot of them because the 18-month horizon to make an SRO takes careful monitoring and planning, as well as a steady drumbeat training for standing that watch - if you notice at month 14 that a member is far from qualification or has largely ignored the card, well, there's nothing you can do to make up the previous 14 months of lost time.
3) The reduced SSDF requirements shouldn't really impact nukes. Again, on a boat that has a well-run small arms program, this requirement was being almost entirely met by the forward duty section, who have so many people that they complain when they have more than 1 watch on a duty day. The aft duty sections are generally already close to the minimum as it is for emergency reactor startup purposes. You mentioned in your post that watchstanders are already port/stbd watches, so I don't know how you think the reduced SSDF manning is going to make that better. The impact of the new rule is that forward duty sections can stay 4-section while sending more personnel to school and may be able to go 5-section on occasion, but my bet is that institutional inertia causes the COB to say no and the XO/CO are too busy to check him.