Obviously BIRT cannot find the Arial font on Linux, which seems naturally.
If you want to use the font, you need to install the Arial font on the Linux server.
However, you should check if the licensing conditions for the font allow this.

Fonts are searched using the fontsConfig.xml file.

I recommend to use a different font instead if your server runs on Linux, e.g. one of the Liberation fonts.
You can also add entries to the config file which will automatically replace uses of Arial with eg. Liberation Sans,
like this:

The liberation fonts look slightly different, but are designed to have the same glyph widths as the MS fonts.
Maybe for bold, italic, bold-italic you need additional entries, I don't remember...

How can I convert the PDF ...?

Once you created a PDF, you cannot simply exchange fonts, because the glyphs have different width and height in different fonts.

For the font alias settings in fontsConfig.xml, is this done on my device (Windows) or on the server (Linux)?

The font mapping always happens at runtime, it's not baked into your rptdesign. So, the fontsConfig.xml is considered on the device where BIRT is running. While developing on Windows, it's on your machine, when running on Linux, it happens there.

Regarding where the file is located, I cannot help you, I'm not using Tomcat. But a quick search on the web should give you an answer.