Although the ATSF "Big" domes and the UP dome fleet never came under Amtrak ownership, both sets of cars actually operated under short term lease in the first month or so on Amtrak trains operated by ATSF and UP respectively until other cars could be substituted.
Amtrak eventually "owned" a total of 111 of the domes built. At Inception, they purchased 95 domes - 80 of them from BN, which was the entire BN fleet (CB&Q-43, GN-17, NP-16, SP&S-3, WP-1(via CB&Q)). The other 15 were 6 from AT&SF, 2 from B&O, 3 ex C&O(from SCL), and 4 ex WABASH(from N&W).
Additional purchases were 4 Milwaukee "Super Domes" in 1972, 5 SP domes in 1972 and 1973 (they had been leased at inception), 1 ex C&O dome from Autoliner Corp in April 1974 after a lease in 1972-73, 3 domes from D&RGW after the "RGZ" terminated in July 1983, and finally 3 more Milwaukee "Super Domes" in 1990 after Princess Tours abandoned the "California Sun Express".
Some domes never saw service and were scrapped without ever getting to Amtrak paint, but the majority served for a period and then were sold off. The last 3 "short" domes were sold to the Alaska RR in July 1999, and as of the year 2000, only the single CB&Q and two GN full dome lounges still operated in Amtrak livery (ex MILW 53 "Mt. Mitchell" also operates on the "Piedmont" in Amtrak colors, but is owned by NCDOT). During 9/2001 the CB&Q and one of the GN full dome lounges were sold to American Orient Express, leaving only 10031 (ex GN 1391 "Ocean View") running on Amtrak.
Also, during the early years Amtrak "mandated" that any PV moving in an Amtrak operated train had to be in Amtrak colors. An example shown here is WP 882 "Silver Planet" (never owned by Amtrak) operating for Los Angeles County in Amtrak operated commuter service as the LA-108 "San Fernando".
The numbering scheme applied by Amtrak referenced different types and sources of the cars - i.e. the ATSF cars were 935x, GN/CBQ full domes 936x, SP domes 937x, etc. Observations, lounges, sleepers, etc got broken up into various subsets. Coaches were numbered based on capacity - i.e. 940x were 40 seat CBQ cars, 942x were B&O 42 seaters, 944x thru 948x (they had too many cars) were 46 seat coaches of DRGW, CBQ, GN, SP&S & NP, 950x cars were CBQ 50 seaters, 954x were 54 seat CBQ cars, and 956x were Wabash 56 seat coaches.