I understand what you're saying.  There's always a trade-off between having things "just work" which often involves adding a lot of exceptions and special cases, versus keeping behavior consistent and simple but forcing people to take extra steps on their own.

In general the more complex that underlying behavior the more I like to keep things consistent and simple and avoid special cases.

But, maybe this is a situation where the confusion of the simple behavior warrants adding a special case.

But my point is that $$ is NOT (intended to be) special to make.  That's why make doesn't do parentheses matching which it sees it.

In other words, to make this:

bye: $$(hello#world)

is treated the same way as this:

bye: D(hello#world)

for any character "D".  It's not special to make at all and so we don't do anything special with the parens either.

I don't think it's inconsistent because that's what escaping a character means: none of its special features are in force.  Personally I think it would be inconsistent to treat an escaped "$" differently than any other character.

I will look at the fix but I'm not sure I want to try to work around this.  If "$$" appears in the prerequisite list then it's not special to make... this is true regardless of whether second expansion is enabled or not.

As with all special characters the best way to mask them is by hiding them in a variable:

$ cat Makefile
sem = ;
hash = \#

.SECONDEXPANSION:
all: who $$(shell echo hi 1>&2 $(sem) echo there 1>&2);@:
who: $$(shell echo 'hi $(hash) there' 1>&2);@:

$ make
hi
there
hi # there

Or of course you could put the entire thing in a variable which is even simpler/cleaner:

$ cat Makefile
sem = $(shell echo hi 1>&2 ; echo there 1>&2)
hash = $(shell echo 'hi # there' 1>&2)

.SECONDEXPANSION:

all: who $$(sem);@:
who: $$(hash);@:

$ make
hi
there
hi # there

I'll need to think about whether adding more special casing to try to recognize and manage variables/functions targeted at secondary expansion is going to cause other issues.

Parser chokes on second expansion of a prerequisite with ; o #

$ cat makefile
MAKEFLAGS+=--warn-undefined-variables
.SECONDEXPANSION:
hello: $$(shell echo world;)
        touch $@

bye: $$(hello#world)
        touch $@
$ make hello
makefile:7: * unterminated variable reference.  Stop.
$ make bye
makefile:7: * unterminated variable reference.  Stop.
$


Parser treats ; as a recipe delimiter and # as a comment delimiter.