I’ve personally used the midi din in and out directly with the pyramid without any issue.
do you have a reference for that claim… has @squarpadmin acknowledged this?
I think creating some kind of ‘myth’ that the din is unreliable is extremely unhelpful, unless its an acknowledged issue - and with some proper details.
why is this unhelpful?
because, more often than not (in the years we have had the pyramid) the issues turn out to be either user issues or something related to their setup, or even the instruments they are driving.
but this ‘myth’ would be a simple way to shortcut this , and say ‘oh its the optocouplers’, rather than getting to the bottom of the issue.
also, how reliable is this - what if this ‘fact’ has come from a particular user, who happened to have a pyramid with a damaged optocoupler i.e. its a one-off (or even infrequent) hardware issue… or they just simply misunderstood the issue.
so please let’s not start repeating things that “I read somewhere” without something more concrete to back it up.
of course, if you have some solid information, this would be useful information (perhaps in a separate topic) - and also something that I think would be useful to discuss with @squarpadmin , so we can determine when and where it is likely to be an issue.
as for the above issue…
Im a little confused about what is being said, the OP seems to be quite related to a specific instrument and @Epicycles issue, id say at first glance is probably not related.
it/s not helpful to just lump ‘random midi issues’ in one topic… there are lots of us using the pyramid regularly (and have for years) without issue… so there is very unlikely to be a ‘generic’ midi issue that would have gone ‘unnoticed’ for so long.
usually when we see these issue its is specific combinations of devices, and frankly, invariably its some setting or issue on the controller or synth… which is, unfortunately, more common than you’d expect.
this means, its important for these issues to be very detailed very specifically, and not ‘muddy’ the waters with (potentially) unrelated issues.
as for the issues, as I said hard to track… but
generally, when I see note on/off getting ‘confused’ , this is almost always due to a previous note off some how being dropped… it gets really wacky, you get things like a synth, playing notes when you release a key, and silencing when you press it 
(sending an all-notes-off, will often bring the synths back into ‘sync’ , at least in my setup)
this is not specific to they pyramid, I’ve seen it in setups without any sequencer involved.
for me invariably, its caused by some midi feedback, or something else which overwhelms the midi data traffic (but usually its a feedback loop)… if these loopbacks do not involved clock, they can sometimes be quite hidden… as the system works fine, except for every now and then missing a note off…