I had the same problem with my app that uses i18n. First of all: Angular is still beeing developed, so for example i18n doesnt work out of the box, depending on what you want to do here is a roadmap for i18n on GitHub #16477 maybe still in version 5 they want to implement dynamic translation so you won't need a different app for each language, but thats a different issue ;)
I suppose youz are looking for:
--output-path
with this command you set the path where your actual files will be stored (from Angular wiki)
--base-href only sets the href attribute in your index.html but since you want to set the path for the files you need to use --output-path
I'm not sure if you also need to set --deploy-url for your apps, anyway --deploy-url /en creates the following index.html:
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Title</title>
<base href="/">
<meta name="viewport" content="width=device-width,initial-scale=1">
<link rel="icon" type="image/x-icon" href="assets/favicon_link_icon.png">
<link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
<link href="/en/styles.xxx.bundle.css" rel="stylesheet"/>
</head>
<body>
<app-root></app-root>
<script type="text/javascript" src="/en/inline.xxx.bundle.js"></script>
<script type="text/javascript" src="/en/polyfills.xxx.bundle.js"></script>
<script type="text/javascript" src="/en/main.xxx.bundle.js"></script>
</body>
</html>
--output-path ./dist/en creates a new folder dist/en with almost the same index.html only the src path is missing the /en/ prefix
