For any better/additional idea, I would, that goes without saying, give full credit.
This being said, my musings certainly are of general interest, since even if you do just SOME macros, here and there, with any (free or paid) tool, the same probs will quickly arise, although to a lesser extent.
Now, as stated before, I've heavily been into AHK macroing lately.
Thus, I have to copy with numerous sw's internal key shortcuts / shortkeys, and also with their respective menu shortcuts (Alt-xyz).
And of course, I always try to assign identical / similar commands to the same shortkeys, in different programs, i.e. I either re-assign the original shortcut (if such re-assignment is available) to my "standard" shortkey for that function, or I intercept the (un-re-assignable) shortcut of a given applic, and then reassign it to my standard AHK shortcut for that function.
Now, bec of various internal shortcuts in many progs, such a system will quickly create an almost incredible mess: In many progs, I've got hours and hours to work on re-assigning their multiple internal shortcuts, or to simply get away with them (which is a pity, and which is in order to not them interfering with my AHK macros... ok, with AHK, this is technically not possible, thank God, i.e. AHK key (combination) assignments will prevail, but I', not able, from my personality, to "overwrite" internal shortkeys, without bothering about such things, so I have to look them all up, one by one, and notwithstanding any further development of my macro system: so you easily understand all this is a conceptual nightmare...).
As described here, trying to overlay your personal macro system, to your set of possibly 100 applics and tools of any kind, is virtually impossible, so what can we do?
In this connection, I tried various ways of administering at least my own macros (let alone the internal shortkeys of every given prog), by sorting in spreadsheets, by doing comments in my macro lines, then filtered by editors/regex, etc. - chaos it remains, and for every changes in my macro system (which occur daily), I would have to search for possible incompatibilities (with native shortkeys) in dozens of applics. As said before, it's a nightmare.
So, what's a viable STRATEGY to macroing?
I've adopted this one: For every applic, I delete/reassign/note any Alt-Fkey combination, i.e. I do NOT accept any alt-F-key shortkey in any of my applics: I "need" them for my own macros, and this comprises Alt combinations.
Then, for every applic that is NOT "calculation", i.e. except for calculators, spreadsheets, statistical sw and so on, I "sacrify" the numkey block, and whilst /, *, -, +, numenter and numcomma/dot have global assignments, the ten digit keys there are all available for individual shortkey assignments of the particular applic in focus; it goes without saying that wherever possible, I assign often-used commands to numkey keys, whilst lesser-used commands "go" to Alt-Fkey keys.
Also, I've sacrificed the 4 keys F9 to F12 to "global scope", i.e. have reassigned any applic-specific key assignments from them to some other key (combination); the same is true for "special keys" like "PrintScreen", "Pause" and such.
This is to say that I deliberately refrain from doing "mnemonic" key combinations like "control-alt-p" and the like, instead heaving to memorize some "Num9" for some command, in order to not have to endure the above-described chaos, triggered by happily mixing up your own macros, and "native" applic-bound short-keys all over the "place" = all over your keyboard.
To tell you the truth, for the time being, I have also preserved (i.e. not yet reassigned) a dozen or so shift-control-xyz key combinations, all for global var(iable) toggles of my AHK system, and that obliges me to also check for such shift-control-combinations in any of my applications, but from my experience, in most such applics, these are very rare, so perhaps I'll even maintain those.
I also have got a Cherry 4700 keypad, since it's the only low-price keypad out there which is "programmable", i.e. to which keys you can reassign other key combinations which then will be interceptable by AHK: shift-control-alt-a... in my case, i.e. cramped combis never ever originally assigned by any applic of my knowledge.
From the above, you see that my point is, try to separate, as far as possible, your own macro system (which you will have to memorize, more or less, notwithstanding the fact that at the beginning, and for rarely-used commands, perhaps in rarely-used applics, you will need some sort of reference table system, be it on screen, be it on paper), from any possible shortcuts from your various applics - use (perhaps) shift-control keys, use alt-F keys (and yes, for special commands not that much similar to commands in other applics, why not assign them to "unused" Alt-combis in that particular applic? = nor yet assigned to a (useful-to-you) command there, neither (and especially) to a menu shortcut over there)... and be brash* enough to sacrifice your numkeys in every applic where you won't enter digits but here and then anyway - and any macroing will become so much more straightforward for you!
* = How come some Continental knows such terms? Well, it's a remembrance from an Auden poem in Visconti's Conversation Piece (1974, and no, not on YT (yet))