Because Quark and Supplementaries are such big mods in this pack, changes to those will impact the pack a lot. I love the consistent updates (and bug fixes) from both.
To preface all of my opinions, I love automation, including Botania, Create, Quark, and many other automation playthings.
Concerning specifically Musketeer, getting magma cream is a pain, at least from my experience. In my experience, I made a double chunk slime farm so I can get slimes spawning.
Big slimes get pushed up and fall into a snow powder and magma cream pit. Only medium magma cubes and larger drop magma cream, and slimes split on dying, so only large slimes can make magma cream.
Anything smaller than big slimes hop forward to the iron golem and into the soul campfires.
All items are collected with hopper minecarts and output to copper pipes to pipe them up to the surface.
This is probably way too much magma cream and slime than you'll ever need, but I have trouble imagining an alternative. Like... luring slimes into a pit and killing them manually? It was a fun community project to mine out a chunk for this so I dunno if I'm too pained over this.
Additionally, farming glow berries for Toretoises and glowstone dust is a pain. This is an issue with Quark but it affects Musketeer. The only way you can efficiently farm glow berries is to use bone meal and harvest it manually with right-click.
Toretoises are a pain because they eat a random amount of glow berries, rather than a fixed amount, which makes automating Toretoises much more difficult, plus, Quark has (or had?) a bug where Toretoises simply do not automate.
Lastly, I don't know if or how to change this, but having only backpacks is a bit painful for large-scale builds. I'm used to shulker boxes with everything I need. Maybe I'm not fully adapted to backpacks, bundles, and rails to transport me to get things faster.
Tangentially, I love quat's Packages a lot and would love to see it in any pack I play, even if it's nerfed or configured. I love having inventory blocks that don't open a GUI, such as Crucial 2's crate.