1.  "if the template is put into the startup folder and becomes, in effect,
the normal.dot"  This is not correct at all.  A template in Startup is a
global template.  Technically, it does not affect normal.dot - although of
course it may contain code that does.  Normal.dot is still, well, normal.dot.
Global templates are essentially code containers.

2.  global templates are not "open" in the normal sense.  Word parses the
code modules in a global and makes the procedures available, globally.
However, the file itself is NOT open.  This is why the project is
"unviewable".  The ONLY template that has viewable code modules while the
file is unopened, is normal.dot.  ALL other template/document code modules
must have the file itself open in order to view/modify code.

So to answer your two questions:

a) "how can I make sure those references are in the code" - by putting the
References into the template.  References are not really "in" the code.  The
project has references.  So...put the references in.  I am not quite
following what the problem is.

b) "and how can I view the code when opened from the startup folder"  Again,
a Startup .dot file has its code modules accessible to execute, but the file
is NOT open.  You must open the file itself to view/modify code.

My globals always have either a button, or a keyboard shortcut, that opens
the file itself.  I do this for easy access to it so I can, in fact, modify
code.

Note:  modified code in a global is immediately accessible as such.