The Mishna Berura 32:110 writes that lechatchila one should be careful not to leave a space of 3 yudim between words, since according to Rabenu Tam this is a space worthy of a parsha stuma.
I have noticed many old csavim [especialy from Lubavitch] that didn't care even lechatchila to leave a vacant space of 4-5 yudim between words, and were not choishesh of this shita (even lechatchila).
I think the explanation for this opinion is, A. the basic shiyur of 3 letters mentioned by RT was 3 big letters like beitin, not small letters as yudim. B. since the soifer is accustomed to large revachim for spacing each parsha [9 letters, no less] leaving a small 3-5 yud space, will not resemble at all a shiyur parsha.
I explained these issues elsewhere, and it is difficult on the blog to write in length.
I did add a bit to this in my hebrew blog
פורום לנושאי סת"ם: ריוח ג' יודי"ן בסת"ם