Include colored box, rotated text in booktabs styled table

MWE, which reproduce this (unusual) table (as you shown in question) is:

documentclass{article}
usepackage[table,xcdraw]{xcolor}
usepackage{rotating}
usepackage{makecell, multirow, tabularx}
newcolumntype{L}{>{raggedrightarraybackslash}X}
usepackage[skip=1ex]{caption}

begin{document}
    begin{table}[htb]
    centering
    setlengthextrarowheight{2pt}
    settowidthrotheadsize{Text 4}
    renewcommandrotheadgape{}
begin{tabularx}{0.6linewidth}{ l llll c@{,}X }
    Xhline{1pt}
            & multicolumn{4}{c}{Header 1} 
                                && cellcolor{gray!25}     
    Xcline{2-5}{0.6pt}
                &   rothead{Text 1}
                    &   rothead{Text 2}
                        &   rothead{Text 3}
                            &   rothead{Text 4}
                                &&  cellcolor{gray!25}%
                                    multirow{-2.2}{=}{noindent
                                    Some line 1 Some line 2
                                    Some line 3}         
Header 3    &   &   &   &   &&  Header 3                
    Xhline{0.6pt}
A           &   &   &   &   &&  1                       
B           &   &   &   &   &&  2                       
    Xhline{1pt}
end{tabularx}
    end{table}
end{document}

Addendum:

documentclass{article}
usepackage[table,xcdraw]{xcolor}
usepackage{rotating}
usepackage{makecell, multirow, tabularx}
newcolumntype{L}{>{raggedrightarraybackslash}X}
newcommandmrrc[1]{multirow{-2.4}{*}{rothead{#1}}} % <---
usepackage[skip=1ex]{caption}

begin{document}
    begin{table}[htb]
    centering
    setlengthextrarowheight{2pt}
    settowidthrotheadsize{Text 4}
    renewcommandrotheadgape{}
begin{tabularx}{0.6linewidth}{ l llll c@{,}L }
    Xhline{1pt}
            & multicolumn{4}{c}{Header 1} 
                            && cellcolor{gray!25}    
    Xcline{2-5}{0.6pt}
            &   &   &   &   &&  cellcolor{gray!25}                 % <---
                                smalllinespread{0.84}selectfont  % <---
                                multirow{-1.8}{=}{noindent
                                    Some line 1 
                                    Some line 2
                                    Some line 3}    [1ex]
Header 3    &   mrrc{Text 1}       % <--- rotated headers moved down
                &   mrrc{Text 2}
                    &   mrrc{Text 3}
                        &   mrrc{Text 4}
                                   &&  Header 3     
    Xhline{0.6pt}
A           &   &   &   &   &&  1                   
B           &   &   &   &   &&  2                   
    Xhline{1pt}
end{tabularx}
    end{table}
end{document}

hopefully produce what you like to have:

Is it what you want to have?

documentclass{article}
newcommand*turn{rotatebox[origin=b]{90}}
usepackage{array}
usepackage{booktabs}
usepackage{multirow}
usepackage{array, caption}
usepackage{graphicx}
usepackage{makecell}
usepackage[table,xcdraw]{xcolor}

begin{document}

begin{table}[]
centering
begin{tabular}{@{}llllll@{}}
toprule
& multicolumn{4}{c}{Header 1} & 
cmidrule(lr){2-5}
&multirowcell{3.5}{turn{Text1}} &multirowcell{3.5}{turn{Text2}} &multirowcell{3.5}{turn{Text3}} & multirowcell{3.5}{turn{Text4}} & cellcolor{gray!25} makecell{Some line 1 Some line 1 Some line 1 Some line 1 Some line 1} 
addlinespace
Header 3 & & & & &Header 3
midrule

& & & & & 
& & & & & 
bottomrule
end{tabular}
end{table}

end{document} 

Here is a solution with {NiceTabular} of nicematrix.

documentclass{article}
usepackage{xcolor}
usepackage{makecell}
usepackage[skip=1ex]{caption}
usepackage{nicematrix}
usepackage{booktabs}

begin{document}
begin{table}[htb]
centering
setlengthextrarowheight{2pt}
begin{NiceTabular}{llllll}[code-before = rectanglecolor{gray!20}{1-6}{2-6}]
toprule
 & multicolumn{4}{c}{Header 1} 
 & hphantom{Some line 3}
   Block{2-1}{makecell{Some line 1 Some line 2  Some line 3}}    
cmidrule(lr){2-5}
 & rotate Text 1
 & rotate Text 2
 & rotate Text 3
 & rotate Text 4 
Header 3    &   &   &   &   & Header 3 
midrule
A           &   &   &   &   &  1 
B           &   &   &   &   &  2 
bottomrule
end{NiceTabular}
end{table}
end{document}

• This solution uses booktabs (nicematrix is compatible with booktabs). Hence, it's easy to use shorten the cmidrule with cmidrule(rl) (there is no need of a dummy column).

• The command Block of nicematrix put its content at the mathematical center of the merge cells. There is no need to adjust manually as in multirow.

• In nicematrix, the colored panels are drawn before all the rules (the output is better in the PDF viewers: the rules won't seem to disappear at some levels of zoom in some PDF viewers as Adobe Reader).