I found the reason but to make a patch is beyond my powers.
When I used the steps described below, I got this in console:
 
NOTE: Window with stalled focus found!, faking focus-out event
NOTE: Window with stalled focus found!, faking focus-out event
Hint: (lazarus) [TBuildManager.SetBuildTarget] Old=x86_64-linux-gtk2 
New=x86_64-linux-qt FPC=False LCL=True
HERE1 lpQT
Hint: (lazarus) [TBuildManager.SetBuildTarget] Old=x86_64-linux-qt 
New=x86_64-linux-gtk2 FPC=False LCL=True
HERE2 lpQT
HERE3 lpQT
Hint: (lazarus) [TBuildManager.SetBuildTarget] Old=x86_64-linux-gtk2 
New=x86_64-linux-qt FPC=False LCL=True
Note: (lazarus) deleted backup "/home/v1/Lazarus_Qt/lazarus/lazarus.old"
Note: (lazarus) renamed file "/home/v1/Lazarus_Qt/lazarus/lazarus" to 
"/home/v1/Lazarus_Qt/lazarus/lazarus.old"
Info: (lazarus) Execute Title="Build IDE"
Info: (lazarus) Working Directory="/home/v1/Lazarus_Qt/lazarus/"
Info: (lazarus) Executable="/usr/bin/make"
Info: (lazarus) Param[0]="idepkg"
Info: (lazarus) Param[1]="-w"
HERE4 lpQT
Hint: (lazarus) [TBuildManager.SetBuildTarget] Old=x86_64-linux-qt 
New=x86_64-linux-gtk2 FPC=False LCL=True
HERE5 lpQT
Hint: (lazarus) TMainIDE.DoRestart 
LAZARUS END - cleaning up ...
Hint: (lazarus) [TMainIDE.Destroy] B  -> inherited Destroy... TMainIDE
Hint: (lazarus) [TMainIDE.Destroy] END
Heap dump by heaptrc unit
3185022 memory blocks allocated : 308622317/315523376
3185022 memory blocks freed     : 308622317/315523376
0 unfreed memory blocks : 0
True heap size : 1572864
True free heap : 1572864
TLazarusManager.Run starting /home/v1/Lazarus_Qt/lazarus/lazarus ...
Hint: (lazarus) [TMainIDE.ParseCmdLineOptions] 
PrimaryConfigPath="/home/v1/.lazarus"
Hint: (lazarus) [TMainIDE.ParseCmdLineOptions] 
SecondaryConfigPath="/etc/lazarus"
Hint: (lazarus) [TBuildManager.SetBuildTarget] Old=x86_64-linux-gtk2 
New=x86_64-linux-gtk2 FPC=True LCL=False
TComponentTreeView.SetSelection: Updating component node values.
TLazSourceFileManager.InitOpenedProjectFile select form in designer: 
Form1:TForm1 TDesigner
NOTE: Window with stalled focus found!, faking focus-out event
NOTE: Window with stalled focus found!, faking focus-out event
See several "Hint: (lazarus) [TBuildManager.SetBuildTarget]..." about changing widgetset.Lines 
"HEREx lpQt" are from me, they indicates that state of 
MiscellaneousOptions.BuildLazProfiles.Current.TargetPlatform); is unchangedThe changes come from method 
MainBuildBoss.SetBuildTargetProject1 which is called several times in main.pp, mainly in 
TMainIDE.mnuToolConfigBuildLazClicked at line 4595.It calls TBuildManager.SetBuildTarget and nested function 
GetEffectiveLCLWidgetType where is line: Result:=FBuildTarget.CompilerOptions.GetEffectiveLCLWidgetTypeIt is 
probably the reason why combobox in "Configure Build Lazarus" is ignored and is replaced by value 
from Compiler Options.V.______________________________________________________________
Od: Vojtěch Čihák via Lazarus
Komu: Lazarus mailing list <[email protected]>
Datum: 02.01.2018 22:21
Předmět: Re: [Lazarus] Rebuilding IDE Gtk/Qt

Thanks to zeljko for confirming.
 
I was able to reproduce right now:
 
I have my Lazarus 1.9.0 r56925M FPC 3.0.4 x86_64-linux-qt.
I started new project. I saved it. I open Project Options -> Addition and Overrides and 
added LCLWidgetType "gtk2".
I run the project once just to see it is really GTk2 - it is.
Now I enter Tools -> Configure Bulid Lazarus. Options are Debug IDE, LCL 
WIdgetType = qt. I don't change them.
I switch to "Clean common files" and click Build.
After restart I have Lazarus 1.9.0 r56925M FPC 3.0.4 x86_64-linux-gtk2.
 
V.
 
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