Yes it does matter where the port is placed, particularly in the situation you describe. You can definitely have both Helmholtz resonation and quarter-wave standing wave resonation, simultaneously.Martin King has a spreadsheet that is designed to model this exact scenario, so you might want to download it and explore your options if you are considering this kind of system. I used it to model the two π tower, although I was trying to do the exact opposite thing you are talking about. I wanted to position the port and driver to minimize quarter-wave resonances, so that the only thing that had influence was Helmholtz resonance. Sounds like you want to maximize quarter-wave resonance in addition to Helmholtz resonance.
To me, the two mechanisms are pretty similar really. The standing wave nodes of a horn or pipe act much the same as Helmholtz resonation, so neither is "better" to me. I make horns, which are very similar to standing wave pipes, essentially a wide-band form of them. I also use bass-reflex speakers, which use Helmholtz resonators. The only reason I wanted to limit the standing wave nodes in the two π tower was that I had chosen to work with the Helmholtz property and to use it to tune the box. But since the box is tall and thin, standing waves will result inside and I wanted to position the elements where the nodes had the least influence.
With Martin King's spreadsheet I was able to accomplish this, and measurements of impedance and response show it is purely a bass-reflex box as a result. If I hadn't placed the driver and port in the right position and used damping material in the box, the speaker may have had unintended resonances that made it act differently than I had intended. So I was impressed with the ability of the MJK spreadsheets to model the effects of standing waves inside the box.