Well there you are totally wrong as Skyrim has the exact same problem, if anything it's even worse because only the last file is applied, compatibility patches are required to make mods work together if they chamge the same files.
I have very little experience of the Witcher 2, but one advantage to editing the Vanilla files is using the User Content folder. This appears toallows you to name a file the same as the games (player.ws, movable.ws, combat.ws, etc) but only contain your changes to be applied to the original.
Mods though would need the same compatibility patches that Skyrim does.
So obviously the compatability isn't the reason for Witcher 2 modding being so small. Linear mechanics is one major factor and 2 years late with RedKit the other.
Actually Skyrim was quite modular as far as modifications go: for example you can modify the iron sword entry in one mod and the steel sword one in another they'd work just fine together (unless you have wild or dirty edits which is the fault of the modder for not cleaning their mod). I wouldn't be able to hit the 255 ESP/ESM limit if this wasn't the case
Sadly this isn't true with most other games where all the swords data might be stored in one file for example. This was an issue with Saint's Row 4 for example where part of the weapon data was stored in one common file which made certain mods incompatible. For example a mod that changed a shotgun mesh and a mod that changed an AR mesh weren't compatible, you had to get to the nitty and gritty and edit the xml files that were several thousand lines long yourself, something most people didn't know how to do properly.
Say what you will about Skyrim but the data structures used for mods and how they interact with eachother is pretty well thought out for the most part. My main beef with it is the scripting, more specifically how it bakes certain data into your saves and how it handles script run time allocation.
TW2 was far from perfect modding due to how it handled data. This is immediately apparent if you read the FCR mod description on nexus and why it's not more modular. I know this isn't the best comparison but if you were do do one between SkyRe for Skyrim and FCR for TW2 (both mods focused on changing combat, leveling and character build mechanics): SkyRe is less than 130 MBs in size and this is with new meshes and textures included while FCR is over 1.4 GBs without any of that as far as I know. Don't get me wrong, I'm not taking a jab at TW2 or the modder behind FCR (Flash is working for CDPR now, he knows what he's doing), but you can't really say Skyrim had major compatibility problems unless mods modified the same thing or had strange interactions with eachother (which are mostly easy to fix with TES5Edit if you know what you're doing).