1) to get the tooltip popup to work I assume there must be some stylesheet 
for this. Did you include this?
2) I can think of no reason why the tooltips and the backlinks should not 
work simultaneously, i.e in the same wiki. 
3)...However, do you mean that you want the backlinks to show* inside the 
tooltip popup*? If that is the case, the popup must also show the backlinks 
viewtemplate. However, the viewtemplate must "think" that it is inside the 
correct tiddler. This is done with the TiddlerWidget. So your code would be 
something like:

<div class="tooltip">
bla bla
<div class="tooltiptext">
<$transclude tiddler="Tiddler 2" mode="block"/>
<$tiddler tiddler="Tiddler 
2">{{||$:/.giffmex/ViewTemplate/refslinks}}</$tiddler>
</div>
</div>


<:-)

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