Does port location make a significant difference with regard to speaker placement?

Based on the picture in your profile, that's a good looking system! The distance of your speakers from the wall looks pretty good too. 

A handful of things (you probably know many of these):
1. Is the base still muddy when you turn off the sub? If no, and assuming you don't have a high pass filter on your mains, the sub may be the culprit.
2. Is the base still muddy when you stick a sock in the speaker ports? Many speakers/subs come with foam inserts to tailor the sound of the bass region. 
3. What feet are you using on the Monitor Audio Silver 6 and the sub? I placed Herbies Threaded Gliders under my speakers and some Hudson Hi-Fi feet under my sub, and those made a giant difference in cleaning up my muddy bass. Speaker/sub isolation is essential for me.
4. To hit the price point of ~$1000, the Monitor Audio Silver 6 make some compromises. The bass region may be one of those compromises, so an upgrade may be in order since you're looking for that next level up in quality. 

I essentially agree with clearthinker. Ports are a way of pushing the bass cut off a little lower at the expense of a much steeper cut off. I have never heard a ported loudspeaker produce what I consider to be accurate bass.
With todays high powered amplifiers,  DSP and the incredible drivers we have today you can make a sealed woofer/subwoofer do almost anything you want without any port noise. 
Clearthinker in my experience 30 Hz is asking a bit much of a panel speaker. I roll my Sound Labs off at 120 Hz to sealed subwoofers. The Sound Labs will go down to 40 Hz nicely if a bit on the lumpy side but removing the bass from them creates a large improvement in midrange and treble clarity not to mention headroom. How many ESLs have you seen do 110 dB without vaporizing? Another benefit is that distance from the front wall becomes less critical. 

Not sure where you are located-common oversight when OPs ask for
some ideas-They may well miss out on an opportunity to meet another
member right next door. 

Admin- Can you make a short list of suggestions people will read
prior to submitting a question?

RMAF is still on. Change your tickets!

I've had the MA Silver sizes.  Delightful.  Yes, if you plug them they will sound better in near wall placement.

@classdstreamer good questions and thanks for the compliment.  
1) Sub is not in the 2 channel mix currently - that's a future tweak, moreso when I step up to a nice REL or ??
2) Since pic was taken I've added Gaia 1's
3) Haven't tried plugging the port but that's on the agenda for tonight.  
4) I hear you on upgrade, but will say I listened to a $12K set of speakers the other day and was thinking system to system they were no beter than what I had....these do punch way above their weight class.  So far the only speaker that really wowed me as a clear upgrade was the Focal Sopra 2, which size wise might be an issue.