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What you mean?
The object which modder can read, to treat and to change (for ex. through S3D) is not the controller... it's the named part of code (part of parameters), which the true controller (hard coded) uses for work...
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It's difficult to me to discuss programming questions on english... therefore i have finished my speech... 
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The object which modder can read, to treat and to change (for ex. through S3D)
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1)The bits that you describe, may indeed be an object (3D), but can also be descriptions (Alphabetical fields) or numeric values (numeric fields).
S3D provides the interface, courtesy, as we all know, of skywasjer.
2) I refer you to the first page of skywasjer's interface, line 2) on the right, in red.
I also refer you to any of the StateMachineClass "Graph" files in SH3's Library.
Click on the first node, read the (type) number in the top right hand section.
It's type 10, and the name for type 10. . . is controller.
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it's the named part of code (part of parameters). . .
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. . . refer to part 1)
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which the true controller (hard coded) uses for work...
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The true controller that you refer to is not actually called the controller.
Some of the generally accepted names are. . . routine, sub-routine, method, function, procedure.
These names describe a section, or chunk, of program code, written to fulfill a specific function (or functions) within a program.
Where the procedure ( or any of the above descriptions ) is relatively simple, preferably uses the same values, and outputs the same result each time, the procedure may be replaced or substituted by a Macro instruction/procedure.
If you are confused by the dual use of the word "Function", it is simply that a procedure fulfils a function ( or functions ), but a procedure can also be CALLED a function, and a procedure can also CALL a function, which is another procedure.
I understand that your knowledge of English is limited, but as a second language, it's more advanced than my second language, so congratulations.
But if i understand you correctly, you are in fact calling a procedure. . . a controller.
If a program is written well, and structured to be easily editable by someone unfamiliar with that particular program, each procedure ( or function ) will be preceeded by explanatory notes written by the original programmer, and headed. The heading for the programmer's notes describing the StateMachineClass code, may well "name" the procedure "StateMachineClassController", or something similar, but these notes, including the heading
will be enclosed within parenthesis, so the program doesn't attempt to read it as part of the code, and crash.
I don't know where you got the name controller for the hard code, because i haven't seen the hard code, nor should i, and therefore nor do i want to.
On the subject of code, i have tried to put an IF, THEN, ELSE condition in the parameters of a zone in the Zones.cfg, just on the off chance that the fields would act on it, but it became obvious that the Zones.cfg just consisted of alphabetical fields for the zone descriptions, and numeric fields for the parameters.
But then hell, without seeing the hard code, i wouldn't know till i tried.
Come to think of it, the effects parameters reads alpha and numerics, so i'll try that later, just in case.
It'll never work i know, but then, as i said i won't know till i try.
If the effects fields will understand an IF, THEN, ELSE as actions, it could be as simple as:
IF ShipDamageState=State_Dead . . . (send it off to the SMC controller to check conditions)
THEN FloodingTime=1800 . . . . . . . . . (slowly flood undamaged zones of dead boat)
ELSE FloodingTime=650 . . . . . . . . . . (normal flood time if ship not dead but zone damaged.)
Now that sounds mad, and linking it all together reliably is not gonna be that simple,
but all i need is for SH3 to understand that statement in some form, wherever i can get it to understand it, (even if it's nowhere near the zones.cfg), linked to the conditions and/or a timer, which will flood previously undamaged zones on a dead boat . . . and job done.
A tall order maybe, but has anybody tried?
But i digress...
Anvart,i've written the above descriptions for program code so that next time you want to explain what a procedure is to someone, you'll know what to call it.
Unfortunately i at least hope, that what i've written is of more assistance to you, than you've been to me.
Maybe in six months or so, after i've cracked it, you might see fit to throw me a relevant crumb.
Of course if i DO find a solution to the sinking problem, obviously you won't want it.
Fair do's.