I think it's not unreasonable to expect that using filters to reduce the number of displayed rows in a table would have a impact on other tables's positions, just as if rows had been added or deleted. That seems like a valid feature request to me.
The other approach I thought about may depend on the nature of the tables you're building... If it's just a Totals table at the bottom you could put those into Footer Rows - these are rows that are displayed at the bottom of a table, would automatically scale based on the displayed rows, and wouldn't be affected by the filter.
Here's an example I threw together:

The 'Back-End' table is pretty straightforward... a list of all the options and their prices. A simple calculation in the Total field works out the price if the corresponding Qty cell is > 0
The Customer table has four critical elements attached:
1) The full table has to have at least as many rows as the Back End table (or, more specifically, at least as many rows as you'd ever likely want to show).
2) One Footer row (Via Inspector -> Table -> Headers and Footer. Here I have it set to 1, so the bottom row is fixed.
3) The formula in cell A2 is:
=FILTER('Back-End'::A:E,'Back-End'::D>0,"")
This performs the first-level filter - it extracts all the data from Back-End::A:E where the value in column D is > 0 (i.e. there's a quantity set).
This has the effect of pulling all the non-0 quantity lines into this table (with a chunk of blank lines afterwards, like:

Which brings us to...
4) A filter is applied to this table to filter out any rows that are blank:

So now the empty rows in the table are suppressed. However, you still have a Totals row since that is part of the footer. In this row (or rows - you can designate up to 5 footer rows) you can put your blurb, Totals, signature lines, etc.
The filter is dynamic - as soon as you set a quantity on any other row in the Back-End table, it will automatically appear in the Customer Table (and disappear if the Qty is set to 0 or blank).
Here you can see I've set a Qty of 4 for item 'r', and it's added to the table, as well as expanded the footer to 5 rows with a signature/approval line:

(since the table is highlighted, you can also see the suppressed rows 9 through 40 since they're blank and filtered out).
This doesn't help if you want more than 5 rows at the footer, but hopefully this does get closer to what you're trying to achieve..?