Yes, directives from http://angular-ui.github.io/bootstrap are highly customizable and it is easy to override one of the templates (and still rely on the default ones for other directives).
It is enough to feed $templateCache, either feeding it directly (as done in the ui-bootstrap-tpls file) or – probably simpler – override a template using the <script> directive (doc).
A contrived example where I’m changing alert’s template to swap x for Close is shown below:
<!doctype html>
<html ng-app="plunker">
<head>
<script src="http://ajax.googleapis.com/ajax/libs/angularjs/1.0.5/angular.js"></script>
<script src="http://angular-ui.github.io/bootstrap/ui-bootstrap-tpls-0.4.0.js"></script>
<script src="example.js"></script>
<link href="https://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-combined.min.css" rel="stylesheet">
<script id="template/alert/alert.html" type="text/ng-template">
<div class="alert" ng-class="type && "alert-" + type">
<button ng-show='closeable' type="button" class="close" ng-click='close()'>Close</button>
<div ng-transclude></div>
</div>
</script>
</head>
<body>
<div ng-controller="AlertDemoCtrl">
<alert ng-repeat="alert in alerts" type="alert.type" close="closeAlert($index)">
{{alert.msg}}
</alert>
<button class="btn" ng-click="addAlert()">Add Alert</button>
</div>
</body>
</html>
Live plunker: http://plnkr.co/edit/gyjVMBxa3fToYTFJtnij?p=preview