Hello, everyone. This is my first post here on this helpful site. I hope my posts will be useful.
I don't think it's a particularly "big" hole you would be digging with your custom layout. Based on my experience and what Samantha, Frank and Bill have written, it'd be more like a divot---it might trip you up a little but you couldn't get buried in it. You could have the reed positions changed later. It's possible, though, that with a standard layout, your new instrument would be attractive to more potential buyers if you chose to resell it.
I understand your wanting to have the ability to run a number of notes on the pull without awkward fingering. I've discovered, however, that certain tunes, to flow smoothly, force me to use fingerings that seem awkward at first. In fact, just holding the darn little box was awkward for me, at first.
I have a Jeffries layout Morse C/G. You described a pulled run including the right hand B, C#, and D. I often play that run like Jim Lucas described it. That and other similarly tortuous fingerings become relaxed and easier after practice, as Frank mentioned, and really help me to appreciate the possibilities of my instrument. I've also come to appreciate that reversing bellows direction, even when I don't "need" to, can improve a tune's flow by limiting bellows stretching and as a consequence, lessening air button usage and the associated sound effects that come with taking "breaths," although I'm far from perfecting that technique.