Palette 2 with an Ender 3 Printer
On this thread, Does anyone tried Palette 2.0 on Creality Ender 3 or Ender 3 Pro?, there are a couple of useful links:


There is a video, albeit for the CR-101, but that should be of help: YouTube - Setup Guide: Creality CR-10 with Palette 2;
In addition, this Facebook group, Mosaic Palette, Palette+, Palette 2 (Pro) Users, apparently has some users who have paired their Ender 3 with the Palette 2.


However, with respect to your question about the flow rate and steps/mm, there isn't much info out there about that, and no one seems to have experienced similar issues, but your issue might have something to do with profiles - which, as you haven't mentioned them in your question, it is hard to know if that might be the issue or not. 

In the same thread, this post, states:


  I use it with the Ender 3.  There is a profile in Canvas and Chroma for it also. 


This link here, Chroma for Palette 2, states that after using Cura, you then need to load the G-code file into Chroma v3.1, after having selected the appropriate profile. However, if you use Canvas, then there is no need for Cura nor Chroma, as Canvas can slice. This link goes through the whole process for Benchy.



At the risk of repetition, the process for preparing the print, post-slicing, is also given here, from Multicolor 3D Printing How To: Using the Mosaic Palette+ with the Creality Ender 3, albeit slightly different from the link above:


  Setting Up Chroma:
  
  When you load up Chroma, you’ll be presented with a blank canvas ready
  to be filled with your 3D creations.  In the top left corner, make
  sure that you have the Ender 3 selected from the drop down menu. 
  After this you can click Load Print.  From there you’ll be presented
  with your gcode files that you have on your computer.  
  
  In this example we will be selecting the butterfly-1.gcode file, and
  clicking Open.  From here Chroma will be compiling and arranging the
  settings for the gcode file to be displayed.  This might take a minute
  or more.
  
  Selecting Your Colors:
  
  Once the loading is completed, you will be presented with the 3D
  rendering of our butterfly!  This butterfly will be in 4 randomly
  selected colors by default, but we will be changing this next!  To
  change the colors, navigate to the top of the screen where you will
  see 4 colored circles, and drop down arrows along with each circle. 
  These circles represent the colors of each tool head.
  
  To change the color, click on the Tool Head Colored Circle, and your
  options for color will appear, we’re going to select Black for our
  first color.  After this, you will want to select the Default PLA
  Settings by clicking the Drop Down Arrow to the right of the first
  Tool Head Colored Circle.  
  
  As we make these changes you will notice that the 3D rendering of our
  butterfly will change to our corresponding colors.  Repeat this
  process for the remaining 3 Tool Heads, remember to use the Default
  PLA Settings for each Tool Head.
  
  Saving Your Project:
  
  After you have selected all your colors, you will click Save for
  Printer in the top right corner of Chroma.  From there, name your
  file, and click Save.  You will be then presented with a loading bar
  as Chroma prepares our 2 output files.  One of the files will be an
  adjusted gcode file that has added the purge tower we just modified,
  and the other file will be a file that goes straight to the Mosaic
  Palette+.
  
  Printing Your Project:
  
  Once the files are ready, you will be presented with a screen that
  says “Ready to Print!”.  On this screen you will be presented with the
  files you have created for your project, which for us are the
  butterfly-1.msf which goes to the Mosaic Palette+ and the
  butterfly-1.msf.gcode file which is your newly created gcode file.
  You will also be presented with “Materials Used” for the project,
  “Number of Splices” for the project, and “Number of Pings” for the
  project.
  
  After this, you will need to turn your Creality Ender 3 on if it isn’t
  already.  After making sure that you have all your components set up
  and assembled correctly, then it is safe to begin the printing
  process.
  
  Depending on your specific project will determine how long the
  printing process takes.  But once your printing process is complete
  you will be presented with your beautiful multicolored 3D butterfly
  (or whatever your project was)!  After printing is finished, you
  should let the project cool before you attempt to remove it from the
  tray. Once it has cooled you can now gently pry the project off of the
  tray.




Footnotes

1 The CR-10 is, on a broader level, an Ender-3 with 2 lead screws and a slightly different board.