foundtrinket(x) - Found a trinket. x is the trinket ID (1-20 usually). The ID is hard to grab in a custom level, bruteforce if you're uncertain and see which is removed. 21+ will increase the trinket counter but not actually give any trinkets - in case you want secrets for 105%+ trinket completion 
In the normal game, 2 maps has more than one layout.
Do you mean that one of the trinkets is erased from the level after using that command? If yes, then where was the trinket

(or

) found, in the main game? It uses that command in there, am I right? And if you use that command with x>20 after getting all the trinkets, does it show "Twenty One"? I have read about a code that contains a list of the numbers for the trinket counter, like "Zero", "One", "Two", etc. It contained "Twenty One", but not "Twenty Two", etc. and that produced the 21st trinket glitch. It was fixed in v.1.1, but I don't know if "Twenty One" is still in the code. Did you try using that command with x>20 twice? I wonder what that does...
2 maps? Do you mean Dim. VVVVVV and the Polar Dimension? Does the Polar Dim. have alt sates too?
Also, I don't understand the difference between ifflag and customiffflag (and with iftrinkets too).
Btw: In one of my previous posts in this thread, I wrote "agile". I didn't want to write that!

I might have written the words too fast and then one was corrected automatically to "agile".

Just ignore that word.