the theme in your screenshot is designed to show as it appears. so it is not the problem with the theme. it is a problem only if the theme does not appear as it was coded to appear.
the number of custom fields is the choice of the user because every user has different needs as per the rules of their country. Manager cannot provide all fields as default.
if the line spacing is your issue, you can simply adjust the same in your theme.
{% for field in custom_fields %}
<tr>
<td colspan="99">
<div style="font-weight: bold; padding-top: 20px">{{ field.label }}</div>
<div>{{ field.text | newline_to_br }}</div>
</td>
</tr>
{% endfor %}
just reduce the value for padding-top to a lower value as per your requirement.
also, you can make the custom field heading and text appear side by side rather than one below the other. see the code below.
{% for field in custom_fields %}
<tr>
<td colspan="99">
<div style="padding-top: 20px"><b>{{ field.label }}</b> {{ field.text | newline_to_br }}</div>
</td>
</tr>
{% endfor %}
there are a lot of possibilities in Manager if you know liquid coding. also you can hire someone locally who knows liquid coding to customize the themes for you.
in short, the PDF generator in Manager has no issues. it generates PDF as per the code in your theme.
Correct code = Correct PDF
Wrong code = Wrong PDF