I think you're reading

our $foo = 1;
BEGIN {...}
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as: allocate some memory and initialise it to 1 and you expect it to happen at parse/compile time but you should think of it as just a shorthand for

our $foo;
$foo = 1;
BEGIN {...}
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so the memory is allocated at compile time but the initialisation happens at runtime, which will be after all the BEGIN blocks have run.

It might seem like a good idea to initialise $foo to 1 at the same time as allocating the space but then you run into problems like

our $foo=sub_which_hasnt_been_compiled_yet();
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