Can't say I've ever thought of Barclay and Murdock as the same character.
It's clear the actor got his fame from the Murdock role though he did refine it for TNG. Both characters are very eccentric, such that they can be considered not all there or socially impaired. They are, however, eccentric in very different ways. Murdock is more the manic eccentic with very wild & crazy ideas and actions, Barclay is more of a subdued eccentric, a shrinking violet, but his emotional behavior is very manic. Barclay is much more the classic nerd/programmer/engineer with difficulty relating to/understanding other people. I see the two characters as variation on a theme. It's not 100%, but a clear piece of it is there. He turned all the Murdock character's eccentrities inward to create a very intelligent but awkward engineer with a wild degree of fears & insecurities, Barclay. They're like the yin & yang of the same set of underlying concept (smart vs. not too bright, introverted vs. extroverted, fearful vs. fearless)
One can see similarities between Sisko and Hawk (A Man Called Hawk, the series that put him on the map, though it was a spinoff of his role on, what was that, Spenser or The Equalizer?). A number of actors don't tread very far from what makes 'em famous (not many, but more than a few). There are some similarities between Hannibal & Banacek for example, a certain smartass aspect, even though the 2 characters are very different (ah, now I have The A-Team theme stuck in my head). I think they feel if it played well over how many seasons, it should continue to play well or they feel uncomfortable not having an element of that character around, unsure they can achieve popularity without some piece of that earlier character.