2nd layout makes more sense to me, especially if the 4 post ends up as storage more than current project/repairs.
When I bought my building it had a 10ft drop ceiling in it which I was fine with as my first lift only went up to 9ft. I since picked up another that went up 14ft. Then I had some tornado damage and it pushed me to pull the drop ceiling, so now the ceiling is at 16ft. I picked up 5 sections of pallet racking as that is all I could fit and afford last year. It made a huge difference in the shop. I have 3 shelves per rack, so 15 x 32sqft + ( a couple racks are 9 and 12 ft long) more floor space.
The biggest thing I did not realize with them is that it takes a ton of room in front of them to use them. I have 50-100 sheets of material on them for jobs and they are mostly 5x8ft. So, with the depth of the sheet plus the length of the lift, I need a min of 13-14ft in front of the rack to get material on or off. If I have to turn into or out of it, I may need a bit more. It is what it is, but I was a bit surprised with that. It only matters as my building is narrow by long, and when you have a car or truck opposite the racks, it gets narrower. I have 3 of the sections that are long term storage, but the 2 I am trying to use often as WIP, so I do need to deal with it often. I am probably going to get more racks in the next year, will probably even make a mezzanine of sorts in one area just to reclaim even more floorium.
I think with the 2nd layout it will allow you the most flexibility, you won't be stuck with only being able to get one machine to a rack. It seems your experience is like mine and having only the 1 machine option you will end up stuck if it doesn't run right then. I think you will use the Namco first if it will reach just because it will be the nicest to operate and wiggle around in the shop, but being able to use the other easily too is well worth changing it up.