Can the colour change in litmus paper be explained by conjugated systems?
You have shown the structural change in bromothymol blue upon deprotonation.     

For the anion of 7-hydroxyphenoxazone, the following resonance structures involving a p-quinone imine are conceivable: 



The assumption that the $\pi$-system of the neutral species and the corresponding anion are identical is not justified.

A smaller system, in which a similar effect can be observed, is 4-nitrophenol. A solution of the phenol is colourless, whereas the solution of the phenolate is yellow ($\lambda_{\mathrm{max}}$ = 405 nm). 

Again, loss of a proton leads to tautomerism with contribution of a quinoid structure.