What options can I overide in .htaccess ?

All options normally possible in .htaccess are allowed.

Can I have a custom made httpd.conf ?

Yes. In certain circumstances, this can be desirable for some sites. This is possible. the account's httpd.conf is located in:
/udb/acount-name/httpd.conf
you can read it and request a new one or the diffs by submiting it to tech support, in a plain text email. As a general guideline, any changes that do not affect the security and has a minimal impact on performance is acceptable but not guaranteed.

Medium accounts and higher running their own http server (IHPG), do not need to ask, and edit their httpd.conf directly, and also control apachectl directly.

I need a secure SSL certificate

If you already have one from Thawte, verisign or another party, we can install certificates. 128 bits are strongly recommended. If you do not have one, we offer a full rane of certificate services. For security reasons, we generate only 128 bit SSL certs, however we accept to install older certificates. See the pricing scheddule of certificate services.

How can my users have a personal URL like http://mydomain.xyz/~username/ ?

By default all users created from the interface have such an URL. The username is the login name, which is usually different from his/her email. If the default login name is not the way you want it to look, you can create a web alias the following way: using FTP or SSH, go to your home directory, and then go into the "condo" subdirectory. Create a symlink (shortcut) that points to the actual login name. For example from SSH:
cd ~/condo
ln -s username othername
now browsers can use the URL http://mydomain.xyz/~othername/
The 2 web addresses point to the same thing. multiple aliases are possible.