There are a couple of ways to do color separations for screen preparation in Illustrator. You're trying to do it the more complicated way, so I'll walk you through how I'd do that first.
Let's start with a simple text object that has a fill and a stroke on top of a rectangle:
The Long Way
Step 1: BACK UP YOUR ORIGINAL ARTWORK!
This process will make ...
Select your black objects.
Path → Combine.
Select your line.
Path → Stroke to Path.
Make sure that your path is above your black objects (Object → Raise to Top).
Select your path and your black objects.
Path → Difference.
If desired, Path → Break Apart.
Okay, so straight from the horses mouth - there is no "flatten" feature. Seems like a fairly basic operation to me!
"There isn't a merge command like in Photoshop, but as a workaround you can create a new empty layer, drag everything else to inside that layer and then go to Layer -> Rasterize..."
PDF,as SVG files, actually, don have the concept of "layers".
In SVG files there are groups of objects - Groups are meant to be more flexible than layers - and what Inkscape calls "Layer" is rather an UX choice - if you check the generated SVG file, you have a group there, not distinguishable, but for specific inkscape metadata, from a group created by ...
If you are publishing your work as email, generally speaking, you have to roll back your ambition to the most basic HTML page, or even to putting in a simple PNG or JPEG bitmap of the entire document, perhaps with slices, depending on how complicated your design is. You also need a plain text version of your document for email readers that either don’t ...
If you want to save it as a flattened file, i.e. a file that no longer contains layers, then you just need to uncheck the 'Create Acrobat Layers from Top-Level Layers' option in the save as PDF dialogue...
N.B. This may have a slightly different name or location depending on your version of Illustrator, Adobe have a habit of moving these things around.
If Pathfinder > Merge does not work...or Object > Flatten Transparency does not work... or a combination of the two.... you are left no other options but to processes objects in sections/pieces. There's no other solution I'm aware of.
Overall thoughts, all I can do really as we don't have any details or screengrabs to understand your situation other than at an overview level:
1. If you have a lot of transparency effects, sometime a last step can be flattening transparency.
2. You can often save large file sizes when you have repeating or iterating elements by using Symbols.
3. Simplify ...
There's no shortcut way to do this, you could however use the method mentioned above, just make sure you duplicate the layers before you flatten them to bitmap.
2 shortcuts are still better than a whole set of clicks I guess?
Try this: (only works with vector)
Select all your vectors, go to Object>>Flatten transparency. This will make all vectors closed, so the outlines.
This wil make a top object cut all the objects behind it and so on.
See the picture below.
You actually want to Select All, then Pathfinder > Merge, then Object > Ungroup if needed. You should then be able to move things around on layers and have "holes" or "counters" where lower layers need to show through upper layers.
The merge command will combine all objects which have the same fill and remove any content which may be hidden below ...
It may not be possible, depending on the artwork, but if you were to make a copy of the file and create shapes based upon the intersections by using any "shape intersection" tool or functionality and then fill those shapes with the closest solid color value to simulate the overlapped colors, then you will have vectors which will not need to be rasterized.
The "flattener - preview" is the right tool to use. The 'Transparent objects' will show objects that have transparency properties (blending modes/opacity less than 100%) and the 'All Affected objects' shows any element that may be affected by some element of transparency. For example some type with a drop shadow. The type itself may not have transparency but ...