To clarify, there are two different issues you're describing:

-- Warning about performance DLLs

-- Temp table use in SSIS

For the first one, this is a warning only and not an error. In most cases, you can open BIDS or SSDT as administrator to resolve the warning.

For the second issue, you've found an inherent issue in SSIS with respect to temporary tables. Because SSIS does a runtime validation before reading from or writing to tables, attempting to read or write temp table data will often result in unexpected behavior, including possibly failing the package. If you need to create temporary storage for ETL, my recommendation is to built permanent staging tables that are truncated (or selectively deleted) at the outset of each load. It takes some extra effort to set this up, but you'll have a more predictable experience when running ETL loads.