That wouldn't match "ALPHA" on a line by itself; it demands a non-# non-_ character before the ALPHA. If you do it this way you probably want a zero-width assertion.

My first thought is to do a global replacement of all the exceptions, to remove them from the data. Then search what's left for the strings you do want to count. Performance-wise I don't know how great this would be, but it's easier to read (and possibly easier to write if it needs to be automated for a large amount of search strings).

while(<>){
   s/(?:_|#|XL5 )ALPHA//g;
   print if /ALPHA/;
}
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edit: davidrw beat me to it.