As the Last Great Time War progressed, the vast majority the Timelords began reconfiguring their Tardis's to combat configurations.
Not only did the external shell alter, but the internal layouts were also changed, becoming darker, simpler, and more militaristic. As new Tardis's were rushed into service using expedited methods, these alterations became the norm.
Only a few Timelords, such as the Doctor, refused to make such changes to their beloved craft.