Hi,
1. You can change that in the Business edition. It's actually one of the main features of the Business edition.
With the Business edition, on the System>Emails menu, the emails can be edited. And when you edit them, you have an interface to customize them. Among the options, you have the "template" setting, which allows you to choose among different templates which are preinstalled. And there are different color versions, in order to more easily adapt the emails to the look of your website.
Now, if you do it manually by directly modifying the files in the media folder, it's a lot more difficult. Also, you'll lose your changes when you update your HikaShop, so make sure that you backup your changes. If you want to change the CSS of the emails, it's probably not in the email file that you want to do that but in the template file being used. So you need to look in the default template file in the templates folder of the mail folder.
The "insert images" setting defines whether the images used in the emails are embedded in the email or if the email just reference them with the URL of the image from your website. So even if you turn off this setting, the look of the emails should normally be the same. If that setting is turned on, the emails will be bigger because of the images. So, with big images it can cause delivery issues. Also, spam filters can be more prone to refuse the emails. With the setting turned off, if the email is visualized while not connected to the internet, or if the email is visualized and the website is not online, or the URL of the website has changed, the images won't be displayed by the email client.
If you don't want the images, you need to remove the corresponding img tags from the different files.
2. Are you sure that you're looking at the emails for the same order ? Also, please note that you might have two numbers for each order: the order number and the invoice number. Please double check.
3. I don't know of a way to have both email not display the options in the same manner. The only reason would be if the emails have been modified in an incorrect manner. So I'm afraid the issue comes from what you changed.