As name suggests Custom layout (CL) is drawing a layout for customized designs say ADC/memories.. Physical design(PD) is process of implementation of RTL to GDS2. layouts are input to PD. With CL, you will be specialized in drawing layout, will get more exposure to layout rules, foundry DRM, challenge lies in reducing area of design at base level. In analogy, PD is process of constructing a house (will all given materials like windows, doors, bricks) and CL is the process of design of only blocks (like bricks, doors, windows).
It is of individual interest to choose between CL or PD. Personally I like PD as each time you face different challenge when going for different SoC. whereas CL is very laborious work. Hope this gives some idea to you.
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