Having tested the mod with SA I have become aware of the following bugs. Apologies if you are already aware of them:

Cimota Restructor YI-Transmutation recipe icons are not scaling correctly (only upper quarter of the icon is showing).
Youki recipes that used to allow productivity no longer accept productivity modules. This includes intermediates.
Youki structures cannot use quality modules for any recipes (the unicomp to resource interconversions might be intentional).
The YI Engines assemblers (C1, Y2 and P3) can no longer make copper cable, power poles, modules, solar panels, accumulators or circuits. Additionally some but not all of the new SA structures (foundry, biochamber, lightning rod, electromagnetic plant and cryogenic plant) are also not included for those three machines.
30x Frumital-R recipe icon is not scaling correctly (only upper quarter of the icon is showing).
YI Beacons do not gain distribution efficiency with quality, unlike regular beacons. This means >12 need to affect a structure to be better than legendary regular ones.
The two tiers of Youki belt have disappeared.

Yuoki, does not technically support SA - yet. Support currently is just for 2.0

Some of these bugs I do know about.. few a I didn't..

For beacons, not sure if ill change this or not.. if you play around with the various tiers of yuoki beacon vs base beacons, there is a few times where the yuoki is better when you start mixing modules around etc... still pondering this one.
Not sure if you noticed, while they don't gain the efficiency factor, they are immune to the overload factor that base ones suffer from too many in one area, which has some mixed results.

Productivity modules is funky I need to dig into that more, lots of stuff in this mod just never really allowed it.
There is also a setting in the mod to let you productivity everything if you prefer.

Changing the mod setting for productivity did not change anything.

Even factoring in the overload they only are better if you use >12 per structure. Compared to normal quality it still takes >5 per structure before there is a benefit. Previously they were outright 10% better and had enough range to layer them twice as thick as regular beacons.

I agree the mastercrafted washing plants were always defective when it came to productivity modules and the toolhead and drillhead using recipes were not set to prevent multiplication of the catalyst if productivity was used on those structures.

I think ill have to look into why productivity is just "broken" overall.. appears 2.0 changed some stuff for that despite not giving me errors (usually the game gives me errors for such changes in 2.0)

Another SA related bug is some stuff is too heavy for putting in rockets when it should not be.

again, mod is not SA ready.. only 2.0 so bugs will exist.

To add on to this, recyclers seem to prefer the Yuoki recipes for vanilla items when deciding what items to return, which breaks some stuff on fulgora, discovered when my base clogged up with coal and N7 dust from recycling batteries.

I acknowledge it will be a longer term goal before the mod is SA ready. I was just trying to flag them up in advance.