I think the syntax of the functions is pretty much fine like this, just a bit of optimization work to do on the implementation.

However, a few notes on coding style:

The correct if clause syntax is like this:

if ()
{
    //something
}
elseif ()
{
    //something
}
else
{
    //something
}

All brackets and keywords are on a new line.
Also, string concatenation:

"string" . "string" . function() . $variable

notice the surrounding spaces around the concatenation operator

LOL, awesome typo :P

simply append the comma by default and do a trim() at the end

early exit

append by default, trim at the end

interesting. I was going to suggest using something else, but it turns out using strpos is the fastest way to check something at the beginning of a string. Basically it's like this:

strpos < strncmp < substr

I'm pretty sure we use substr in a couple places, so I may have to adjust that ;)

insert into select does not support DELAYED, so you have to implement some kind of mode checking.
And since you have to do that anyway, you might just as well merge replace_mode in there as well.

I would just say that maybe for end-user it would be more understandable to name the methods and property
insert_into or even insert instead of into.
otherwise the global seems good. the tests will tell

I still want replace_mode and insert_mode merged. There's no reason to handle them separately.

putting empty lines between the blocks improves readability

ok, I'd do a small hack to make the code simpler.
If there is only one array level (so $values[0] is not an array), wrap it in an array ($values = array($values);).
That way later on you only have to care about multidimensional arrays.
I leave it up to you if you like it like that or not :)

use foreach

that was actually good before. It improves readability of the code if a group of assignments with reasonably similar length on the left side of the assignment has the '=' aligned.

why the wrapping?

keep the empty line pls

Ship It!