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From the standpoint of how the layers are represented in the Calibre hierarchical database, I believe that using Layer to merge the layers and using OR will have the same effect. From a performance standpoint, however, this may not be the case. For large layers in multi-threaded runs, you may find that OR is faster.
There is no way to change that error to a warning. No layer operation permits redundant specification of layers. This is enforced as a protection against inadvertent mistakes.
As an observation, it is unnecessary to do a single-layer OR on original layers because this is done automatically for all such layers that are read into Calibre. In this case, thin_lines isn't going to be different from SRAM_OUTLINE after read-in. If thin_lines is needed as a copy of SRAM_OUTLINE, the COPY or DFM COPY operations may prove useful.
Hope this helps.