1000 Variant per day limit

[DavisMK]

Backstory (we sell POD clothing all printed in house so have a lot of variants)

About 6 weeks ago we were told that there was a new limit for uploading variants via API, 1000 variants a day when your store hits 50k variants. For us that is approximately two designs per day. We were told originally that this was only an API limit and that we should continue to upload via the CSV, so have been doing that no problem, until today when i tried to upload a file and it hit the limit after 5 products. 

Support chat are telling me this limit is now in force across all creation methods and that we have a choice of either upload less than 1000 a day, or upgrade to shopify plus at minimum of $3k a month. 

Has anyone else run into this problem? It seems that the help didn't even know it was a thing until i sent them screenshots of the error, seems like communication on this could be a lot better, the help pages don't mention a limit at all except on the developers API page