I have a mobile menu using traditional mobile menu. Due to a long logo, we've placed menu items below. Is it inconsistent that the hamburger icon does not sit on the same level as the close button? Thanks.
TL:DR: The exact position doesn't matter, what matters is the ease of use for your customers.
There are no such hard UX guidelines as "this element has to align with that element with pixel accuracy". They are only supposed to guide your design in the right direction.
Everything beyond that is visual design and subject to your or your company's styleguide.
With that being said, the most important part is how easy is it for the user to reach / use. How attractive it looks is secondary.
The answer to this question here should be interesting for you too:
It shows that users mostly use the phone single handedly, so consider making the hamburger menu closable by swiping left on it, too.
So all in all, think about user friendliness before attractiveness first.
As long as the close button is easily reachable by the hands of the user it should be okay and "normal" users will not even recognize the placement is not consistent.
Sidenote: I would place the shopping-cart icon in the header to make it more prominent.
And i would also consider redesigning the logo and/or creating a web-friendly version of it that is readable/recognizable in smaller size.