I think you can maximally use the WRF-Chem data with MCIP with the way you are set up (BTRIM=0), but the dimensions will differ because of the methods used by WRF and SMOKE to count the dimensions. (Whether it’s a good idea to maximally use the WRF domain in SMOKE is a different conversation.)
To start, the apparent reduction by 2BTRIM + 2NTHIK + 1 is going to result in a reduction of 3 when BTRIM is set to 0. NTHIK is the thickness of the boundary perimeter used in the SMOKE and CMAQ domains. While NTHIK can be flexible because of the way it is coded, in practice, NTHIK is 1. So, 2(0) + 2(1) + 1 = 3.
As it turns out, by reducing the dimension by 3, you will actually use all of the WRF domain. Here is why. In WRF, the lateral boundary cells (i.e., the picture frame with boundary forcing around the perimeter of the domain) are included as part of the full domain dimensions. That is, when you visualize any of the fields on 2D horizontal surfaces, the outermost grid cells around the perimeter of the domain are boundary cells, and those cells are strongly influenced by the information in the wrf_bdy files. Boundary-condition-influenced cells are just part of the main WRF output.
However, unlike WRF, CMAQ (and SMOKE) do not include the boundary cells as part of the “main” domain dimensions. When you omit the one-cell picture frame (which is two cells in each dimension), then those data are used to populate the CMAQ boundary files. The data are still in play for CMAQ; they are just only included in the boundary files rather than both the main domain and the boundary files.
So that’s two of the three. What about the leftover 1?
Well…in WRF, there are really two sets of dimensions in the output: the “unstaggered” and the “staggered” dimensions; you can see this with ncdump -h wrfout, and look at the netCDF dimensions and the global attributes. The “staggered” dimensions are one greater than the “unstaggered” dimensions, and the difference refers to whether you are counting with cell centers or cell faces. In a staggered grid, like the Arakawa C staggered grid used by both WRF and CMAQ, some variables are geolocated at cell centers (most mass and moisture variables), while others are on cell faces (like component winds). In SMOKE and CMAQ, the convention is to use the number of cell centers (or the smaller of the two numbers) to define the grid dimensions. In WRF, either could be used. With MCIP, I use the larger of the two numbers (the staggered number), which reflects the convention that was used by MM5 (the predecessor to WRF). For a long time, MCIP handled both MM5 and WRF data, so it was easier to keep the convention for grid sizes consistent between the models within MCIP.
Hope this helps.