while i have not done this with a millcreek, i have done similar activities with other kayaks.

to your point, there are things that are just easier to do with access. the important thing is to puzzle it through to make sure any part of that is a smart step vs one that you will regret.

the two things i consider:

• will i interfere with the next step or make the next step more difficult if i change the order (e.g., if you still have glueing/epoxying to do, remember that it will not bond with varnish)
• will i potentially make a mess of something that i am then going to need to clean up and essentially redo (e.g. i may have to protect something inside, or redo it, if i spill epoxy on something on the inside)

if you have specific steps that you are considering switching the order on, it may be easier if you propose them for more directed feedback on your ideas.  but it is fairly common that builders, as the build experience, will switch the order of some things around to suit their tastes and make the process easier.

h

   I painted mine early in the build. Almost done now. Two things I'd mention 

1- you will have to cut the tops of the hanging knees flush with the carlins in order to fit the coamings later on

2- if you plan on a sailing component or sailrig leave an approximate 8x8 inch square in the center right behind the forward bulk Unfinished in order to glue the mast step in later on. 
Good luck with the build, PP