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I didnt notice the active layers position thingy... Never used this app before... And Im only using the Viewer; not the full or demo, so its very limited...

I dont see 4-Layers on the file... I see Blue Layer as Top Layer Traces, Green Layer as Bottom Layer Traces; where are the other 1 or 2 Layers of the PCB..? ie the Ground Circuit Layer Mapped out..? The Red Layer is Components, Text, & Ground Circuity (3rd Layer)..? Just trying to figure...

Spent a little time in Photoshop; trying to trace out the PCB... How many layers does your Reproduction board have..?

Do you have Undoctored Photos of Both Sides of the Bare Board..? Im noticing some odd overlays when trying to lay in the Ground Trace in the 2 images in the Zip file...

Got it to open w/ 7zip and DL'd the lay6 Viewer... Going to take a while to compare... -Is this off a Rev.A, B, or C SE Board..?- Edit: Looks like yours is Rev.A; I only have Rev.B boards to compare...

I can see the files in the Zip; but they error when trying to unzip or access in Win10... Where is a safe link to DL Sprint Layout to open the LAY6 file..? I been tinker in PCB Artist...

Hence the last line of my post: "I believe that 12Mb is Obtainable..." I get all that you mention; doesn't negate from the fact that the CPU is capable of addressing 16Mb of RAM/ROM...  Again on paper the CPU is Capable and I stick by my statement that 12Mb could be obtainable... Aside other...

Technically the board/chip could be X-Ray'd... There is also tracing software these days that help trace the board lines out & identify ICs... These older machines are mostly all 2-layer PCB designs & the PDS slot is a dream as it provides direct access to the Data bus lines....

Actually on Paper the 68000 supports up to 16Mb of RAM...  I suspect because of the limited amount of Bus Lines to/from the SIMM Slots is the Limiting Factor for the Base Model SE; that and that the ROM would need Modification to Recognize/Access Limits Higher than 4Mb... IDK; but it is...

Pretty sure I mentioned that it was a Clock Signal Issue in My Prior Post... JS...

What Speed are you running the system bus at..? I noticed the CPU you are using is the later version which can run at high speeds... The system is designed at 7-8Mhz bus speed... When you up the System Bus Speed it gets wonky with the Analog Video Circuity; if you're running a high Clock Speed...