Different guitars sound different - thats the point of different guitars. If you use a real amp - all guitars sound different as well. You can change settings every time you change guitars, but how many do that.
Ultimately, with a single valve amp, you set it up for your main guitar, then use alternate guitars for different tones. If you need the same tone (say for use with a backup guitar) - then you need two guitars the same.
I use a Tele as my main guitar in my current band - but use a PRS CU22 and occasionally a 335 as alternates --- to get THAT flavour of tone for certain songs. They work fine through the same patch but dont sound the same. There not supposed to - they sound like the guitar they are, and in the context of the song I use them in the tone is fine.