I'm not sure I would call 100 million "a few iterations". You appear to have accumulated about a half-second difference, divide that by 100 million and you get a whopping 5 nanosecond difference per iteration if my math is correct. With the difference being so small it may simply come down to the fact that isset
only has one operand in this context and ===
has two.
It's impossible to even discuss the Zend engine's implementation details of the two examples without specifying a specific PHP version; source code is a moving target. Even minute changes to the implementations are going to effect the results over that many passes. I would not be surprised if you found the opposite to be the case on some versions of PHP and/or in a different context.
isset
itself is covered by three different op-codes in the VM depending upon the context:
"Simple" Compiled Variables like your example: ZEND_ISSET_ISEMPTY_VAR
Arrays: ZEND_ISSET_ISEMPTY_DIM_OBJ (requires 2 operands, the var and the index)
Object properties: ZEND_ISSET_ISEMPTY_PROP_OBJ (also 2 operands, var and prop name)
It's an interesting question for curiosity's sake but we're in hair splitting territory and it's probably not a real-world optimization strategy.